| http://purl.uniprot.org/unirules/MF_04077#construct | http://www.w3.org/ns/shacl#construct | "CONSTRUCT {
_:932178 up:source unirule:MF_04077 .
_:932179 up:source unirule:MF_04077 .
_:932180 up:source unirule:MF_04077 .
_:932181 up:source unirule:MF_04077 .
_:932182 up:source unirule:MF_04077 .
_:932183 up:source unirule:MF_04077 .
_:932184 up:source unirule:MF_04077 .
_:932185 up:source unirule:MF_04077 .
_:932186 up:source unirule:MF_04077 .
_:932187 up:source unirule:MF_04077 .
_:932188 up:source unirule:MF_04077 .
_:932189 up:source unirule:MF_04077 .
_:932190 up:source unirule:MF_04077 .
_:932191 up:source unirule:MF_04077 .
_:932192 up:source unirule:MF_04077 .
_:932193 up:source unirule:MF_04077 .
_:932194 up:source unirule:MF_04077 .
_:932195 up:source unirule:MF_04077 .
_:932196 up:source unirule:MF_04077 .
_:932197 up:source unirule:MF_04077 .
_:932198 up:source unirule:MF_04077 .
_:932199 up:source unirule:MF_04077 .
_:932200 up:source unirule:MF_04077 .
_:932201 up:source unirule:MF_04077 .
_:932202 up:source unirule:MF_04077 .
_:932203 up:source unirule:MF_04077 .
_:932204 up:source unirule:MF_04077 .
_:932205 up:source unirule:MF_04077 .
_:932206 up:source unirule:MF_04077 .
_:932207 up:source unirule:MF_04077 .
_:932208 up:source unirule:MF_04077 .
_:932209 up:source unirule:MF_04077 .
_:932210 up:source unirule:MF_04077 .
_:932211 up:source unirule:MF_04077 .
?this up:alternativeName ?name1 ,
?name2 ,
?name3 ;
up:annotation ?annotation5 ,
?annotation6 ,
?annotation7 ,
?annotation10 ,
?annotation11 ,
?annotation12 ,
?annotation13 ,
?annotation14 ;
up:classifiedWith GO:0003700 ,
GO:0003723 ,
GO:0016032 ,
GO:0030430 ,
GO:0044196 ,
GO:0051028 ,
keyword:1035 ,
keyword:1048 ,
keyword:488 ,
keyword:509 ,
keyword:597 ,
keyword:694 ,
keyword:813 ,
keyword:945 ;
up:recommendedName ?name0 .
?name0 up:fullName 'Protein Rev' ;
rdf:type up:Structured_Name .
?name1 up:fullName 'ART/TRS' ;
rdf:type up:Structured_Name .
?name2 up:fullName 'Anti-repression transactivator' ;
rdf:type up:Structured_Name .
?name3 up:fullName 'Regulator of expression of viral proteins' ;
rdf:type up:Structured_Name .
?gene4 skos:prefLabel 'rev' .
?annotation5 a up:Function_Annotation ;
rdfs:comment "Escorts unspliced or incompletely spliced viral pre-mRNAs (late transcripts) out of the nucleus of infected cells. These pre-mRNAs carry a recognition sequence called Rev responsive element (RRE) located in the env gene, that is not present in fully spliced viral mRNAs (early transcripts). This function is essential since most viral proteins are translated from unspliced or partially spliced pre-mRNAs which cannot exit the nucleus by the pathway used by fully processed cellular mRNAs. Rev itself is translated from a fully spliced mRNA that readily exits the nucleus. Rev's nuclear localization signal (NLS) binds directly to KPNB1/Importin beta-1 without previous binding to KPNA1/Importin alpha-1. KPNB1 binds to the GDP bound form of RAN (Ran-GDP) and targets Rev to the nucleus. In the nucleus, the conversion from Ran-GDP to Ran-GTP dissociates Rev from KPNB1 and allows Rev's binding to the RRE in viral pre-mRNAs. Rev multimerization on the RRE via cooperative assembly exposes its nuclear export signal (NES) to the surface. Rev can then form a complex with XPO1/CRM1 and Ran-GTP, leading to nuclear export of the complex. Conversion from Ran-GTP to Ran-GDP mediates dissociation of the Rev/RRE/XPO1/RAN complex, so that Rev can return to the nucleus for a subsequent round of export. Beside KPNB1, also seems to interact with TNPO1/Transportin-1, RANBP5/IPO5 and IPO7/RANBP7 for nuclear import. The nucleoporin-like HRB/RIP is an essential cofactor that probably indirectly interacts with Rev to release HIV RNAs from the perinuclear region to the cytoplasm." .
?annotation6 a up:Subunit_Annotation ;
rdfs:comment 'Homomultimer; when bound to the RRE. Multimeric assembly is essential for activity and may involve XPO1. Binds to human KPNB1, XPO1, TNPO1, RANBP5 and IPO7. Interacts with the viral Integrase. Interacts with human KHDRBS1. Interacts with human NAP1; this interaction decreases Rev multimerization and stimulates its activity. Interacts with human DEAD-box helicases DDX3 and DDX24; these interactions may serve for viral RNA export to the cytoplasm and packaging, respectively. Interacts with human PSIP1; this interaction may inhibit HIV-1 DNA integration by promoting dissociation of the Integrase-LEDGF/p75 complex.' .
?annotation7 a up:Subcellular_Location_Annotation ;
rdfs:comment 'The presence of both nuclear import and nuclear export signals leads to continuous shuttling between the nucleus and cytoplasm' .
?annotation7li8 up:cellularComponent .
?annotation7li9 up:cellularComponent .
?annotation10 a up:Domain_Annotation ;
rdfs:comment 'The RNA-binding motif binds to the RRE, a 240 bp stem-and-loop structure present in incompletely spliced viral pre-mRNAs. This region also contains the NLS which mediates nuclear localization via KPNB1 binding and, when the N-terminal sequence is present, nucleolar targeting. These overlapping functions prevent Rev bound to RRE from undesirable return to the nucleus. When Rev binds the RRE, the NLS becomes masked while the NES remains accessible. The leucine-rich NES mediates binding to human XPO1.' .
?annotation11 a up:PTM_Annotation ;
rdfs:comment "Phosphorylated by protein kinase CK2. Presence of, and maybe binding to the N-terminus of the regulatory beta subunit of CK2 is necessary for CK2-mediated Rev's phosphorylation." .
?annotation12 a up:PTM_Annotation ;
rdfs:comment 'Asymmetrically arginine dimethylated at one site by host PRMT6. Methylation impairs the RNA-binding activity and export of viral RNA from the nucleus to the cytoplasm.' .
?annotation13 a up:Annotation ;
rdfs:comment 'HIV-1 lineages are divided in three main groups, M (for Major), O (for Outlier), and N (for New, or Non-M, Non-O). The vast majority of strains found worldwide belong to the group M. Group O seems to be endemic to and largely confined to Cameroon and neighboring countries in West Central Africa, where these viruses represent a small minority of HIV-1 strains. The group N is represented by a limited number of isolates from Cameroonian persons. The group M is further subdivided in 9 clades or subtypes (A to D, F to H, J and K).' .
?annotation14 a up:Similarity_Annotation ;
rdfs:comment 'Belongs to the HIV-1 REV protein family.' .
?pfs15 up:annotation ?annotation16 .
?annotation16 faldo:begin ?pfsb17 ;
faldo:end ?pfse18 ;
rdf:type up:Region_Annotation ;
rdfs:comment 'Homomultimerization' .
?pfsb17 faldo:position ?thisPositionOn19 ;
rdf:type faldo:ExactPosition .
?pfse18 faldo:position ?thisPositionOn20 ;
rdf:type faldo:ExactPosition .
?pfs21 up:annotation ?annotation22 .
?annotation22 faldo:begin ?pfsb23 ;
faldo:end ?pfse24 ;
rdf:type up:Motif_Annotation ;
rdfs:comment 'Nuclear localization signal and RNA-binding (RRE)' .
?pfsb23 faldo:position ?thisPositionOn25 ;
rdf:type faldo:ExactPosition .
?pfse24 faldo:position ?thisPositionOn26 ;
rdf:type faldo:ExactPosition .
?pfs27 up:annotation ?annotation28 .
?annotation28 faldo:begin ?pfsb29 ;
faldo:end ?pfse30 ;
rdf:type up:Motif_Annotation ;
rdfs:comment 'Nuclear export signal and binding to XPO1' .
?pfsb29 faldo:position ?thisPositionOn31 ;
rdf:type faldo:ExactPosition .
?pfse30 faldo:position ?thisPositionOn32 ;
rdf:type faldo:ExactPosition .
?pfs33 up:annotation ?annotation34 .
?annotation34 faldo:begin ?pfsb35 ;
faldo:end ?pfse36 ;
rdf:type up:Modified_Residue_Annotation ;
rdfs:comment 'Phosphoserine; by host CK2' .
?pfsb35 faldo:position ?thisPositionOn37 ;
rdf:type faldo:ExactPosition .
?pfse36 faldo:position ?thisPositionOn38 ;
rdf:type faldo:ExactPosition .
?pfs39 up:annotation ?annotation40 .
?annotation40 faldo:begin ?pfsb41 ;
faldo:end ?pfse42 ;
rdf:type up:Modified_Residue_Annotation ;
rdfs:comment 'Phosphoserine; by host CK2' .
?pfsb41 faldo:position ?thisPositionOn43 ;
rdf:type faldo:ExactPosition .
?pfse42 faldo:position ?thisPositionOn44 ;
rdf:type faldo:ExactPosition .
?pfs45 up:annotation ?annotation46 .
?annotation46 faldo:begin ?pfsb47 ;
faldo:end ?pfse48 ;
rdf:type up:Modified_Residue_Annotation ;
rdfs:comment 'Phosphoserine; by host' .
?pfsb47 faldo:position ?thisPositionOn49 ;
rdf:type faldo:ExactPosition .
?pfse48 faldo:position ?thisPositionOn50 ;
rdf:type faldo:ExactPosition .
?pfs51 up:annotation ?annotation52 .
?annotation52 faldo:begin ?pfsb53 ;
faldo:end ?pfse54 ;
rdf:type up:Modified_Residue_Annotation ;
rdfs:comment 'Phosphoserine; by host' .
?pfsb53 faldo:position ?thisPositionOn55 ;
rdf:type faldo:ExactPosition .
?pfse54 faldo:position ?thisPositionOn56 ;
rdf:type faldo:ExactPosition .
_:932212 a rdf:Statement ;
up:attribution _:932178 ;
rdf:subject ?this ;
rdf:predicate up:recommendedName ;
rdf:object ?name0 .
_:932213 a rdf:Statement ;
up:attribution _:932179 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name1 .
_:932214 a rdf:Statement ;
up:attribution _:932180 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name2 .
_:932215 a rdf:Statement ;
up:attribution _:932181 ;
rdf:subject ?this ;
rdf:predicate up:alternativeName ;
rdf:object ?name3 .
_:932216 a rdf:Statement ;
up:attribution _:932182 ;
rdf:subject ?gene4 ;
rdf:predicate up:encodedBy ;
rdf:object ?gene4 .
_:932217 a rdf:Statement ;
up:attribution _:932183 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation5 .
_:932218 a rdf:Statement ;
up:attribution _:932184 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation6 .
_:932219 a rdf:Statement ;
up:attribution _:932185 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation7 .
_:932220 a rdf:Statement ;
up:attribution _:932186 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation10 .
_:932221 a rdf:Statement ;
up:attribution _:932187 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation11 .
_:932222 a rdf:Statement ;
up:attribution _:932188 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation12 .
_:932223 a rdf:Statement ;
up:attribution _:932189 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation13 .
_:932224 a rdf:Statement ;
up:attribution _:932190 ;
rdf:subject ?this ;
rdf:predicate up:annotation ;
rdf:object ?annotation14 .
_:932225 a rdf:Statement ;
up:attribution _:932191 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1035 .
_:932226 a rdf:Statement ;
up:attribution _:932192 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:1048 .
_:932227 a rdf:Statement ;
up:attribution _:932193 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:945 .
_:932228 a rdf:Statement ;
up:attribution _:932194 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:488 .
_:932229 a rdf:Statement ;
up:attribution _:932195 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:509 .
_:932230 a rdf:Statement ;
up:attribution _:932196 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:597 .
_:932231 a rdf:Statement ;
up:attribution _:932197 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:694 .
_:932232 a rdf:Statement ;
up:attribution _:932198 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object keyword:813 .
_:932233 a rdf:Statement ;
up:attribution _:932199 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0030430 .
_:932234 a rdf:Statement ;
up:attribution _:932200 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0044196 .
_:932235 a rdf:Statement ;
up:attribution _:932201 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0003723 .
_:932236 a rdf:Statement ;
up:attribution _:932202 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0003700 .
_:932237 a rdf:Statement ;
up:attribution _:932203 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0051028 .
_:932238 a rdf:Statement ;
up:attribution _:932204 ;
rdf:subject ?this ;
rdf:predicate up:classifiedWith ;
rdf:object GO:0016032 .
_:932239 a rdf:Statement ;
up:source unirule:MF_04077 ;
rdf:subject ?pfs15 ;
rdf:predicate up:annotation ;
rdf:object ?annotation16 .
_:932240 a rdf:Statement ;
up:attribution _:932205 ;
rdf:subject ?pfs15 ;
rdf:predicate up:annotation ;
rdf:object ?annotation16 .
_:932241 a rdf:Statement ;
up:source unirule:MF_04077 ;
rdf:subject ?pfs21 ;
rdf:predicate up:annotation ;
rdf:object ?annotation22 .
_:932242 a rdf:Statement ;
up:attribution _:932206 ;
rdf:subject ?pfs21 ;
rdf:predicate up:annotation ;
rdf:object ?annotation22 .
_:932243 a rdf:Statement ;
up:source unirule:MF_04077 ;
rdf:subject ?pfs27 ;
rdf:predicate up:annotation ;
rdf:object ?annotation28 .
_:932244 a rdf:Statement ;
up:attribution _:932207 ;
rdf:subject ?pfs27 ;
rdf:predicate up:annotation ;
rdf:object ?annotation28 .
_:932245 a rdf:Statement ;
up:source unirule:MF_04077 ;
rdf:subject ?pfs33 ;
rdf:predicate up:annotation ;
rdf:object ?annotation34 .
_:932246 a rdf:Statement ;
up:attribution _:932208 ;
rdf:subject ?pfs33 ;
rdf:predicate up:annotation ;
rdf:object ?annotation34 .
_:932247 a rdf:Statement ;
up:source unirule:MF_04077 ;
rdf:subject ?pfs39 ;
rdf:predicate up:annotation ;
rdf:object ?annotation40 .
_:932248 a rdf:Statement ;
up:attribution _:932209 ;
rdf:subject ?pfs39 ;
rdf:predicate up:annotation ;
rdf:object ?annotation40 .
_:932249 a rdf:Statement ;
up:source unirule:MF_04077 ;
rdf:subject ?pfs45 ;
rdf:predicate up:annotation ;
rdf:object ?annotation46 .
_:932250 a rdf:Statement ;
up:attribution _:932210 ;
rdf:subject ?pfs45 ;
rdf:predicate up:annotation ;
rdf:object ?annotation46 .
_:932251 a rdf:Statement ;
up:source unirule:MF_04077 ;
rdf:subject ?pfs51 ;
rdf:predicate up:annotation ;
rdf:object ?annotation52 .
_:932252 a rdf:Statement ;
up:attribution _:932211 ;
rdf:subject ?pfs51 ;
rdf:predicate up:annotation ;
rdf:object ?annotation52 .
}
WHERE {
#baseURI: http://purl.uniprot.org/unirule/MF_04077
#Rule MF_04077 Created by:? on:2017-05-19 Modified by:Edouard de Castro on:2019-11-20
?this up:organism ?thisOrganism ;
rdfs:seeAlso signature:MF_04077 .
?thisOrganism rdfs:subClassOf+ taxon:11646 .
BIND(URI(CONCAT(STR(?this), '#MF_04077a0')) AS ?name0) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a1')) AS ?name1) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a2')) AS ?name2) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a3')) AS ?name3) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a5')) AS ?annotation5) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a6')) AS ?annotation6) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a7')) AS ?annotation7) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a10')) AS ?annotation10) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a11')) AS ?annotation11) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a12')) AS ?annotation12) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a13')) AS ?annotation13) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a14')) AS ?annotation14) .
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch61 faldo:location ?templateMotifSequenceMatchRegionP0461862 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0461864 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04618MF_0407757 .
?templateMotifSequenceMatchRegionP0461862 faldo:begin ?templateMotifSequenceMatchBeginP0461863 .
?templateMotifSequenceMatchBeginP0461863 faldo:position ?templateMotifSequenceMatchBeginPositionP0461858 ;
faldo:reference isoform:P04618-1 .
?templateMotifSequenceProfileAlignmentOperationP0461864 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
?targetMotifMatch65 faldo:location ?targetMotifMatchRegionMatch66 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0407768 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04618MF_0407759 .
?targetMotifMatchRegionMatch66 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0407767 .
?targetMotifMatchRegionMatchBeginMF_0407767 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0407760 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0407768 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_0407757, 1, (STRLEN(?templateMotifCigarP04618MF_0407757) - STRLEN(REPLACE(?templateMotifCigarP04618MF_0407757, CONCAT('^(?:-*[^-]){', STR(((18 - ?templateMotifSequenceMatchBeginPositionP0461858) + 1)), '}'), '')))), '[a-z]', '')) AS ?step169) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_0407759, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407759) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407759, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step169), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_0407759, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407759) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407759, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step169), '}'), '')))), '[^-]', ''))) AS ?step270) .
BIND(((?step270 + ?targetMotifMatchRegionMatchBeginPositionMF_0407760) - 1) AS ?thisPositionOn19) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_0407757, 1, (STRLEN(?templateMotifCigarP04618MF_0407757) - STRLEN(REPLACE(?templateMotifCigarP04618MF_0407757, CONCAT('^(?:-*[^-]){', STR(((26 - ?templateMotifSequenceMatchBeginPositionP0461858) + 1)), '}'), '')))), '[a-z]', '')) AS ?step171) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_0407759, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407759) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407759, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step171), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_0407759, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407759) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407759, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step171), '}'), '')))), '[^-]', ''))) AS ?step272) .
BIND(((?step272 + ?targetMotifMatchRegionMatchBeginPositionMF_0407760) - 1) AS ?thisPositionOn20) .
BIND(?this AS ?pfs1t73) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn19))) AS ?pfsb17) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn20))) AS ?pfse18) .
FILTER ((BOUND(?thisPositionOn19) && BOUND(?thisPositionOn20))) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a16')) AS ?annotation16) .
BIND(?this AS ?pfs15) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch78 faldo:location ?templateMotifSequenceMatchRegionP0461879 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0461881 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04618MF_0407774 .
?templateMotifSequenceMatchRegionP0461879 faldo:begin ?templateMotifSequenceMatchBeginP0461880 .
?templateMotifSequenceMatchBeginP0461880 faldo:position ?templateMotifSequenceMatchBeginPositionP0461875 ;
faldo:reference isoform:P04618-1 .
?templateMotifSequenceProfileAlignmentOperationP0461881 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
?targetMotifMatch82 faldo:location ?targetMotifMatchRegionMatch83 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_0407785 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04618MF_0407776 .
?targetMotifMatchRegionMatch83 faldo:begin ?targetMotifMatchRegionMatchBeginMF_0407784 .
?targetMotifMatchRegionMatchBeginMF_0407784 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0407777 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_0407785 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_0407774, 1, (STRLEN(?templateMotifCigarP04618MF_0407774) - STRLEN(REPLACE(?templateMotifCigarP04618MF_0407774, CONCAT('^(?:-*[^-]){', STR(((34 - ?templateMotifSequenceMatchBeginPositionP0461875) + 1)), '}'), '')))), '[a-z]', '')) AS ?step186) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_0407776, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407776) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407776, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step186), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_0407776, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407776) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407776, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step186), '}'), '')))), '[^-]', ''))) AS ?step287) .
BIND(((?step287 + ?targetMotifMatchRegionMatchBeginPositionMF_0407777) - 1) AS ?thisPositionOn25) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_0407774, 1, (STRLEN(?templateMotifCigarP04618MF_0407774) - STRLEN(REPLACE(?templateMotifCigarP04618MF_0407774, CONCAT('^(?:-*[^-]){', STR(((50 - ?templateMotifSequenceMatchBeginPositionP0461875) + 1)), '}'), '')))), '[a-z]', '')) AS ?step188) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_0407776, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407776) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407776, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step188), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_0407776, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407776) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407776, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step188), '}'), '')))), '[^-]', ''))) AS ?step289) .
BIND(((?step289 + ?targetMotifMatchRegionMatchBeginPositionMF_0407777) - 1) AS ?thisPositionOn26) .
BIND(?this AS ?pfs1t90) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn25))) AS ?pfsb23) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn26))) AS ?pfse24) .
FILTER ((BOUND(?thisPositionOn25) && BOUND(?thisPositionOn26))) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a22')) AS ?annotation22) .
BIND(?this AS ?pfs21) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch95 faldo:location ?templateMotifSequenceMatchRegionP0461896 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP0461898 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04618MF_0407791 .
?templateMotifSequenceMatchRegionP0461896 faldo:begin ?templateMotifSequenceMatchBeginP0461897 .
?templateMotifSequenceMatchBeginP0461897 faldo:position ?templateMotifSequenceMatchBeginPositionP0461892 ;
faldo:reference isoform:P04618-1 .
?templateMotifSequenceProfileAlignmentOperationP0461898 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
?targetMotifMatch99 faldo:location ?targetMotifMatchRegionMatch100 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_04077102 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04618MF_0407793 .
?targetMotifMatchRegionMatch100 faldo:begin ?targetMotifMatchRegionMatchBeginMF_04077101 .
?targetMotifMatchRegionMatchBeginMF_04077101 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_0407794 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_04077102 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_0407791, 1, (STRLEN(?templateMotifCigarP04618MF_0407791) - STRLEN(REPLACE(?templateMotifCigarP04618MF_0407791, CONCAT('^(?:-*[^-]){', STR(((73 - ?templateMotifSequenceMatchBeginPositionP0461892) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1103) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_0407793, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407793) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407793, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1103), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_0407793, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407793) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407793, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1103), '}'), '')))), '[^-]', ''))) AS ?step2104) .
BIND(((?step2104 + ?targetMotifMatchRegionMatchBeginPositionMF_0407794) - 1) AS ?thisPositionOn31) .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_0407791, 1, (STRLEN(?templateMotifCigarP04618MF_0407791) - STRLEN(REPLACE(?templateMotifCigarP04618MF_0407791, CONCAT('^(?:-*[^-]){', STR(((84 - ?templateMotifSequenceMatchBeginPositionP0461892) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1105) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_0407793, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407793) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407793, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1105), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_0407793, 1, (STRLEN(?targetMotifMatchCigarP04618MF_0407793) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_0407793, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1105), '}'), '')))), '[^-]', ''))) AS ?step2106) .
BIND(((?step2106 + ?targetMotifMatchRegionMatchBeginPositionMF_0407794) - 1) AS ?thisPositionOn32) .
BIND(?this AS ?pfs1t107) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn31))) AS ?pfsb29) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn32))) AS ?pfse30) .
FILTER ((BOUND(?thisPositionOn31) && BOUND(?thisPositionOn32))) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a28')) AS ?annotation28) .
BIND(?this AS ?pfs27) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch112 faldo:location ?templateMotifSequenceMatchRegionP04618113 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP04618115 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04618MF_04077108 .
?templateMotifSequenceMatchRegionP04618113 faldo:begin ?templateMotifSequenceMatchBeginP04618114 .
?templateMotifSequenceMatchBeginP04618114 faldo:position ?templateMotifSequenceMatchBeginPositionP04618109 ;
faldo:reference isoform:P04618-1 .
?templateMotifSequenceProfileAlignmentOperationP04618115 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
?targetMotifMatch116 faldo:location ?targetMotifMatchRegionMatch117 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_04077119 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04618MF_04077110 .
?targetMotifMatchRegionMatch117 faldo:begin ?targetMotifMatchRegionMatchBeginMF_04077118 .
?targetMotifMatchRegionMatchBeginMF_04077118 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_04077111 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_04077119 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_04077108, 1, (STRLEN(?templateMotifCigarP04618MF_04077108) - STRLEN(REPLACE(?templateMotifCigarP04618MF_04077108, CONCAT('^(?:-*[^-]){', STR(((5 - ?templateMotifSequenceMatchBeginPositionP04618109) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1120) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_04077110, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077110) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077110, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1120), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_04077110, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077110) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077110, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1120), '}'), '')))), '[^-]', ''))) AS ?step2121) .
BIND(((?step2121 + ?targetMotifMatchRegionMatchBeginPositionMF_04077111) - 1) AS ?thisPositionOn37) .
BIND(?thisPositionOn37 AS ?thisPositionOn38) .
BIND(?this AS ?pfs1t122) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn37))) AS ?pfsb35) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn38))) AS ?pfse36) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn37, 1) = 'S')) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a34')) AS ?annotation34) .
BIND(?this AS ?pfs33) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch127 faldo:location ?templateMotifSequenceMatchRegionP04618128 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP04618130 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04618MF_04077123 .
?templateMotifSequenceMatchRegionP04618128 faldo:begin ?templateMotifSequenceMatchBeginP04618129 .
?templateMotifSequenceMatchBeginP04618129 faldo:position ?templateMotifSequenceMatchBeginPositionP04618124 ;
faldo:reference isoform:P04618-1 .
?templateMotifSequenceProfileAlignmentOperationP04618130 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
?targetMotifMatch131 faldo:location ?targetMotifMatchRegionMatch132 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_04077134 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04618MF_04077125 .
?targetMotifMatchRegionMatch132 faldo:begin ?targetMotifMatchRegionMatchBeginMF_04077133 .
?targetMotifMatchRegionMatchBeginMF_04077133 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_04077126 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_04077134 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_04077123, 1, (STRLEN(?templateMotifCigarP04618MF_04077123) - STRLEN(REPLACE(?templateMotifCigarP04618MF_04077123, CONCAT('^(?:-*[^-]){', STR(((8 - ?templateMotifSequenceMatchBeginPositionP04618124) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1135) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_04077125, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077125) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077125, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1135), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_04077125, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077125) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077125, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1135), '}'), '')))), '[^-]', ''))) AS ?step2136) .
BIND(((?step2136 + ?targetMotifMatchRegionMatchBeginPositionMF_04077126) - 1) AS ?thisPositionOn43) .
BIND(?thisPositionOn43 AS ?thisPositionOn44) .
BIND(?this AS ?pfs1t137) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn43))) AS ?pfsb41) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn44))) AS ?pfse42) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn43, 1) = 'S')) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a40')) AS ?annotation40) .
BIND(?this AS ?pfs39) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch142 faldo:location ?templateMotifSequenceMatchRegionP04618143 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP04618145 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04618MF_04077138 .
?templateMotifSequenceMatchRegionP04618143 faldo:begin ?templateMotifSequenceMatchBeginP04618144 .
?templateMotifSequenceMatchBeginP04618144 faldo:position ?templateMotifSequenceMatchBeginPositionP04618139 ;
faldo:reference isoform:P04618-1 .
?templateMotifSequenceProfileAlignmentOperationP04618145 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
?targetMotifMatch146 faldo:location ?targetMotifMatchRegionMatch147 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_04077149 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04618MF_04077140 .
?targetMotifMatchRegionMatch147 faldo:begin ?targetMotifMatchRegionMatchBeginMF_04077148 .
?targetMotifMatchRegionMatchBeginMF_04077148 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_04077141 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_04077149 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_04077138, 1, (STRLEN(?templateMotifCigarP04618MF_04077138) - STRLEN(REPLACE(?templateMotifCigarP04618MF_04077138, CONCAT('^(?:-*[^-]){', STR(((92 - ?templateMotifSequenceMatchBeginPositionP04618139) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1150) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_04077140, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077140) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077140, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1150), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_04077140, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077140) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077140, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1150), '}'), '')))), '[^-]', ''))) AS ?step2151) .
BIND(((?step2151 + ?targetMotifMatchRegionMatchBeginPositionMF_04077141) - 1) AS ?thisPositionOn49) .
BIND(?thisPositionOn49 AS ?thisPositionOn50) .
BIND(?this AS ?pfs1t152) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn49))) AS ?pfsb47) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn50))) AS ?pfse48) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn49, 1) = 'S')) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a46')) AS ?annotation46) .
BIND(?this AS ?pfs45) .
}
OPTIONAL {
?this up:sequence ?thisSequence .
?thisSequence rdf:value ?thisSequenceValue .
?templateMotifMatch157 faldo:location ?templateMotifSequenceMatchRegionP04618158 ;
edam:is_output_of ?templateMotifSequenceProfileAlignmentOperationP04618160 ;
rdf:type edam:data_0869 ;
rdf:value ?templateMotifCigarP04618MF_04077153 .
?templateMotifSequenceMatchRegionP04618158 faldo:begin ?templateMotifSequenceMatchBeginP04618159 .
?templateMotifSequenceMatchBeginP04618159 faldo:position ?templateMotifSequenceMatchBeginPositionP04618154 ;
faldo:reference isoform:P04618-1 .
?templateMotifSequenceProfileAlignmentOperationP04618160 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
?targetMotifMatch161 faldo:location ?targetMotifMatchRegionMatch162 ;
edam:is_output_of ?targetMotifSequenceAlignmentOperationMF_04077164 ;
rdf:type edam:data_0869 ;
rdf:value ?targetMotifMatchCigarP04618MF_04077155 .
?targetMotifMatchRegionMatch162 faldo:begin ?targetMotifMatchRegionMatchBeginMF_04077163 .
?targetMotifMatchRegionMatchBeginMF_04077163 faldo:position ?targetMotifMatchRegionMatchBeginPositionMF_04077156 ;
faldo:reference ?thisSequence .
?targetMotifSequenceAlignmentOperationMF_04077164 edam:has_input signature:MF_04077 ;
rdf:type edam:operation_0300 .
BIND(STRLEN(REPLACE(SUBSTR(?templateMotifCigarP04618MF_04077153, 1, (STRLEN(?templateMotifCigarP04618MF_04077153) - STRLEN(REPLACE(?templateMotifCigarP04618MF_04077153, CONCAT('^(?:-*[^-]){', STR(((99 - ?templateMotifSequenceMatchBeginPositionP04618154) + 1)), '}'), '')))), '[a-z]', '')) AS ?step1165) .
BIND((STRLEN(SUBSTR(?targetMotifMatchCigarP04618MF_04077155, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077155) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077155, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1165), '}'), ''))))) - STRLEN(REPLACE(SUBSTR(?targetMotifMatchCigarP04618MF_04077155, 1, (STRLEN(?targetMotifMatchCigarP04618MF_04077155) - STRLEN(REPLACE(?targetMotifMatchCigarP04618MF_04077155, CONCAT('^(?:[a-z]*(?:[A-Z]|-)){', STR(?step1165), '}'), '')))), '[^-]', ''))) AS ?step2166) .
BIND(((?step2166 + ?targetMotifMatchRegionMatchBeginPositionMF_04077156) - 1) AS ?thisPositionOn55) .
BIND(?thisPositionOn55 AS ?thisPositionOn56) .
BIND(?this AS ?pfs1t167) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn55))) AS ?pfsb53) .
BIND(URI(CONCAT(STR(?thisSequence), '#position', STR(?thisPositionOn56))) AS ?pfse54) .
FILTER ((SUBSTR(?thisSequenceValue, ?thisPositionOn55, 1) = 'S')) .
BIND(URI(CONCAT(STR(?this), '#MF_04077a52')) AS ?annotation52) .
BIND(?this AS ?pfs51) .
}
}
"xsd:string |
