XB-FEAT-1001094: Difference between revisions
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This is the community wiki page for the gene ''loc100496109'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | This is the community wiki page for the gene ''loc100496109'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
= | =synteny and orthology= | ||
There are 4 genes/loci tandemly duplicated and provisonally annotated as ''cyp27a1'' in ''X. tropicalis'' v10 assembly: | |||
* LOC594905(cyp27a1.3): Entrez Gene: 594905 XP_031749391.1 | |||
* XB1001094 [provisional:cyp27a1]: Entrez Gene 100496109, XB-GENEPAGE-1001094; XP_002933985.3 | |||
* LOC116407844(cyp27a1): Entrez Gene: 116407844 XP_031749759.1 | |||
* XB984297 [provisional:cyp27a1]: Entrez Gene: 100145331 XB-GENEPAGE-984297, XB-GENE-984298 AAI60539.1 | |||
Xtr.chr9: plcd4> znf142< bcs1l> '''LOC594905(cyp27a1.3)'''< grsf1> '''XB1001094[cyp27a1]<''' LOC116407845[Grsf1-like]> '''LOC116407844(cyp27a1)>''' '''XB984297[cyp27a1]<''' wnt6> | |||
=proteins= | |||
The proteins associated with thees Xtrop genes are called 'sterol 26-hydroxylase, mitochondrial' | |||
NCBI Reference Sequences | |||
>XP_002933985.3 sterol 26-hydroxylase, mitochondrial [Xenopus tropicalis] | |||
MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK | |||
MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK | |||
YPMRSDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR | |||
SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNSIFVTIFPPWTNN | |||
LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG | |||
VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDMSSMPLLRAVIKETLRLYPVVPTNSRV | |||
AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR | |||
RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLRFLPRTPSPSA | |||
>XP_002933985.3 sterol 26-hydroxylase, mitochondrial [Xenopus tropicalis] | >XP_002933985.3 sterol 26-hydroxylase, mitochondrial [Xenopus tropicalis] | ||
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AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR | AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR | ||
RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLRFLPRTPSPSA | RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLRFLPRTPSPSA | ||
>XP_031749759.1 sterol 26-hydroxylase, mitochondrial-like isoform X1 [Xenopus tropicalis] | |||
MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK | |||
MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK | |||
YPVRIDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR | |||
SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNYIFVTILPPWTNN | |||
LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG | |||
VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDISSMPLLRAVIKETLRLYPVVPTNSRV | |||
AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR | |||
RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLQFLPRTPSPSA | |||
>AAI60539.1 LOC100145331 protein, partial [Xenopus tropicalis] | |||
AVRQTRAAAGGPSRLGCLPQGRGCGLVQAGRGASVSQGRAVTGAAVGATEGRKEMKEFEDLPGPSLLKNL | |||
YYYFLRGYLLHTHELQLIYKKMYGPLWRSEIGKYKMVNIADPEVLQRLVRQEGKYPMRNKEDVWKAHRDK | |||
RKLAYGPFTEEGHQWYQIRSALNKKMLKPSEAASYAGGINEVVTDFMDRLQDMRKASPSGDMVNDLANAL | |||
YRFAFEGISNIVFETRIGCLDKQIPPETQKFIDSIGYMFKNSVYVTFLPHWTRGILPYWDRYIEGWDNIF | |||
DFGKHLIDKKMSEIQSRLDKGEEVEGEYLTYLLSSANLTMGEVYGSVCELLLAGVDTTSNTLCWAMYHLA | |||
RDPELQQAVYEEVSSAAPMDRIPVAEDIPNMPLLRGVIKETLRLYPVIPTNARIVSEKEVEIGEYRFPKN | |||
TLFVLSHYAIARDEENFEDPLKFKPQRWLRDGGMKHHPFSSIPFGYGVRACLGKRIAELEMHLALSRVIR | |||
MFELRWDPKGEDIKSIARIVLSPSKPVNLQFLERKTHQE | |||
=orthology and synteny= | =orthology and synteny= | ||
Revision as of 10:15, 17 May 2023
loc100496109
This is the community wiki page for the gene loc100496109 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
synteny and orthology
There are 4 genes/loci tandemly duplicated and provisonally annotated as cyp27a1 in X. tropicalis v10 assembly:
- LOC594905(cyp27a1.3): Entrez Gene: 594905 XP_031749391.1
- XB1001094 [provisional:cyp27a1]: Entrez Gene 100496109, XB-GENEPAGE-1001094; XP_002933985.3
- LOC116407844(cyp27a1): Entrez Gene: 116407844 XP_031749759.1
- XB984297 [provisional:cyp27a1]: Entrez Gene: 100145331 XB-GENEPAGE-984297, XB-GENE-984298 AAI60539.1
Xtr.chr9: plcd4> znf142< bcs1l> LOC594905(cyp27a1.3)< grsf1> XB1001094[cyp27a1]< LOC116407845[Grsf1-like]> LOC116407844(cyp27a1)> XB984297[cyp27a1]< wnt6>
proteins
The proteins associated with thees Xtrop genes are called 'sterol 26-hydroxylase, mitochondrial'
NCBI Reference Sequences
>XP_002933985.3 sterol 26-hydroxylase, mitochondrial [Xenopus tropicalis] MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK YPMRSDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNSIFVTIFPPWTNN LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDMSSMPLLRAVIKETLRLYPVVPTNSRV AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLRFLPRTPSPSA
>XP_002933985.3 sterol 26-hydroxylase, mitochondrial [Xenopus tropicalis] MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK YPMRSDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNSIFVTIFPPWTNN LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDMSSMPLLRAVIKETLRLYPVVPTNSRV AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLRFLPRTPSPSA
>XP_031749759.1 sterol 26-hydroxylase, mitochondrial-like isoform X1 [Xenopus tropicalis] MTGLSSLMHSPRLIRNIQAQLTGTMPSASKLGFLPLGRCRWLLHTGRGVSVSQGRAVAGAAVGAVGEEKK MKTFEDLPGPSLLTNIYWVFLRGYILYTHELQAIYKKNYGPMWKSTLGRYKTVNIADVDILETVLRQEGK YPVRIDMEVWKEHRRQRDLSLGPFTEEGHKWHTLRSVLNKRMLKPAEAMLYTGVVNEVVTDFLVRLEEMR SETPSGDMVNDIPNALYRFAFEGISYILFETRIGCLEKQIPVETQRFIDSIGAMLKNYIFVTILPPWTNN LLPYYKRYMDSWDNIFAFGNKLINEKMKKIEARLERDEEVQGEYLTYLISSGKLTDKEIYGSVAELLLAG VDTTSNTLSWALYHLAREPEIQNALYQEVIGVVPGQNIPTSEDISSMPLLRAVIKETLRLYPVVPTNSRV AVEKAITIGDYYFPKDTLIALHHYHISRDEKNFPESDKFIPQRWFRESRVKNNPFSSIPFGYGVRACVGR RIAELEMHMCLSRIIKKYEVRPDPSGAEIKSMARIVLTPHKPINLQFLPRTPSPSA
>AAI60539.1 LOC100145331 protein, partial [Xenopus tropicalis] AVRQTRAAAGGPSRLGCLPQGRGCGLVQAGRGASVSQGRAVTGAAVGATEGRKEMKEFEDLPGPSLLKNL YYYFLRGYLLHTHELQLIYKKMYGPLWRSEIGKYKMVNIADPEVLQRLVRQEGKYPMRNKEDVWKAHRDK RKLAYGPFTEEGHQWYQIRSALNKKMLKPSEAASYAGGINEVVTDFMDRLQDMRKASPSGDMVNDLANAL YRFAFEGISNIVFETRIGCLDKQIPPETQKFIDSIGYMFKNSVYVTFLPHWTRGILPYWDRYIEGWDNIF DFGKHLIDKKMSEIQSRLDKGEEVEGEYLTYLLSSANLTMGEVYGSVCELLLAGVDTTSNTLCWAMYHLA RDPELQQAVYEEVSSAAPMDRIPVAEDIPNMPLLRGVIKETLRLYPVIPTNARIVSEKEVEIGEYRFPKN TLFVLSHYAIARDEENFEDPLKFKPQRWLRDGGMKHHPFSSIPFGYGVRACLGKRIAELEMHLALSRVIR MFELRWDPKGEDIKSIARIVLSPSKPVNLQFLERKTHQE
orthology and synteny
DIOPT/EggNog matches this protein with high confidence to 3 groups of CYPgenes:
1) ~890 seqs from~200species, including Mouse, Pteropus vampyrus (a bat), Otolemur garnettii (a lemur) and Cavia porcellus ( guinea pig) seqs for Cyp27b1, Cyp24a1 and Cyp27a1 ( thus inclusding not'cyp27a'1 as suggested by the provisional name for loc100496109/XB1001094.)
2) genes called Mouse genes Cyp27b1, Cyp11b2, Cyp11b1, Cyp24a1, Cyp11a1, Cyp27a1
and 3) >1700 sequences in >800 species, and the majority of genes/proteens (where named) are called CYP11A1, not'cyp27a1'
Synteny supoorts ....