XB-FEAT-29093450

From XenWiki
Jump to navigation Jump to search

cyp27a1.2

This is the community wiki page for the gene cyp27a1.2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

nomenclature changes

28SEPT2023

Xenopus gene symbol and gene name changed from loc116407844, sterol 26-hydroxylase, mitochondrial-like to cyp27a1.2, cytochrome P450 family 27 subfamily A member 1 gene 2.

This change was based on assessing the CYP27A orthologs and gene duplication in Xenopus and other vertebrates, including 2 frogs ( Hyla Sara and Bufo buff), Human, mouse, alligator and chicken, via Protein alignment, phylogenetic cladogram of proteins sequences and Synteny.

synteny and orthology

25SEPT2023

There are 4 genes/loci tandemly duplicated that were provisionally annotated as cyp27a1 in X. tropicalis v10 assembly:

  • LOC594905 (cyp27a1.3): Entrez Gene: 594905 XP_031749391.1 >> keeps symbol cyp27a1.3
  • XB1001094 [provisional:cyp27a1]: Entrez Gene 100496109, XB-GENEPAGE-1001094; XP_002933985.3 >> becomes cyp27a1.4
  • LOC116407844(cyp27a1): Entrez Gene: 116407844 XP_031749759.1 >> becomes cyp27a1.2
  • XB984297 [provisional:cyp27a1]: Entrez Gene: 100145331 XB-GENEPAGE-984297, XB-GENE-984298 AAI60539.1 >> becomes cyp27a1 aka cyp27a1.1


In X. laevis there are 3x cyp27a1 .L genes:

  • XB984297.L [provisional:cyp27a1] Entrez Gene:446987 XB-GENEPAGE-984297 XP_041432757.1 >> becomes cyp27a1.1.L
  • LOC121398019 , Gene ID: 121398019 (no Xb gene page) XP_041432320.1 >>becomes cyp27a1.2.L
  • cyp27a1 Entrez Gene: 100381137 (no Xb gene page) XP_041433231.1 >> becomes cyp27a1.3.L


In X. laevis.S there is only 1 cyp27a1 candidate

  • LOC108702937 Gene ID: 108702937 XP_041434454.1 >>becomes cyp27a1.3.S

Synteny and phylogenetics using protein accessions support naming these genes in Xenopus as cyp27a1, genes 1-4 as indicated above.

The suffixed serial number is designed to keep genes aligned compared to Human and mouse, so the primary ortholog cyp27a1 gene 1 lies immediately adjacent to wnt6, while the cyp27a1.3 gene is between grsf1 and plcd4 in all species/sub-genomes.

Note: LOC121398283(unch) Gene ID: 121398283 XP_041433230.1 (matches 42 Ensembl seqs from Xenopus tropicalis but none have actual names- just ID numbers- so pretty sure this is NOT a CYP gene)

Synteny pattern

Xtr.chr9 : slc22a3< prkag3< ttll4< cnppd1< abcb6< (NB: no sign of the CYP genes near ttll4) [Chr9:83051487..83122986] ////

Xtr.chr9: plcd4> znf142< bcs1l> LOC594905(cyp27a1.3)>< grsf1> XB1001094[cyp27a1.4]< LOC116407845[Grsf1-like]> LOC116407844(cyp27a1.2)> XB984297[cyp27a1.1]< wnt6> wnt10a>

Mouse CHR1: Stk36> Ttll4> Cyp27a1> Prkag3> > Wnt6> Wnt10a>

Human: TTLL4> CYP27A1> PRKAG3> RPL23AP31> WNT6> WNT10A>

In X. laevis the genes read in reverse are in this pattern:

Xla.Chr9_10L: wnt10a.L< wnt6.L< XB984297.L[cyp27a1.1.L]> LOC121398019[cyp27a1.2.L]> grsf1.L> cyp27a1.3.L> LOC121398283(unch)> bcs1l.L< znf142.L<

Xla.Chr9_10S: wnt10a.S< wnt6.S< grsf1.S< LOC108702937(cyp27a1.3.S)> plcd4.S< LOC108702939(ccr4not)

Table: Xenopus cyp27a1 protein accession and name changes

Based on the cladogram, these changes were made to the 4 paralogs in Xenopus:

species geneID protein accession JBrowse_model_tag > changed to

Xtrop 594905 XP_031749391.1 cyp27a1.3 > cyp27a1.1

Xla.L 100381137 XP_041433231.1 cyp27a1 > cyp27a1.1.L

Xla.S 108702937 XP_041434454.1 LOC108702937 > cyp27a1.1.S

Xtrop 116407844 XP_031749759.1 loc116407844 > cyp27a1.2

Xla.L 121398019 XP_041432320.1 LOC121398019 > cyp27a1.2.L

Xtrop 100145331 XP_002933986.3 XB984297 > cyp27a1.3

Xla.L 446987 XP_041432757.1 XB98429 > cyp27a1.3.L

Xtrop 100496109 XP_002933985.3 XB1001094 > cyp27a1.4

Retrieved from "https://wiki.xenbase.org/xenwiki/index.php?title=XB-FEAT-29093450&oldid=51636"