XB-FEAT-18386060

cyp27a1

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

nomenclature changes

17MAY2023 Xenopus gene symbol changed from LOC594905 [provisional:cyp27a1] to cyp27a1.3

Xenopus gene name changes from provisional ortholog of cytochrome P450 family 27 subfamily A member 1 to cytochrome P450 family 27 subfamily A member 1 gene 3

We are using synteny and protein sequence alignmnet to pre-computed homology groups to infer orthology and inform naming of these genes. See below for more details.

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

These analyses 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)

orthology via matching protein to gene family trees in EggNog5.0

DIOPT/EggNog matches the proteins for the Xtrop genes to 3 groups of CYP genes with high confidence:

1) ~890 seqs from ~200 species, including Mouse, Pteropus vampyrus (bat), Otolemur garnettii (lemur) and Cavia porcellus (guinea pig) seqs for Cyp27b1, Cyp24a1 and Cyp27a1 (ie including cyp27a1 as suggested by the provisional name for XB1001094 and XB984297)

2) Mouse genes called Cyp27b1, Cyp11b2, Cyp11b1, Cyp24a1, Cyp11a1, Cyp27a1

and

3) >1700 sequences in >800 species, and the majority of genes/proteins (where named) are called CYP11A1, not cyp27a1

cobalt protein alignment and cladogram

species protein accession Xtrop XP_002933986.3

Xla.L XP_041432757.1

Xtrop XP_031749759.1

Xla.L XP_041432320.1

Xtrop XP_031749391.1

Xla.L XP_041433231.1

Xla.S XP_041434454.1

Xtrop XP_002933985.3

outgroups

mouse NP_077226.2

human NP_000775.1

frog Hyla sarda XP_056409570.1

Bufo bufo XP_040295327.1

alligator XP_025051106.1

chicken XP_422056.4