XB-FEAT-5837859: Difference between revisions
imported>Xenbase →pvalb.2: Updated nomenclature, replaced: unnamed → pvalb.2 (2) |
|||
| (One intermediate revision by one other user not shown) | |||
| Line 1: | Line 1: | ||
=pvalb.2 | =''ocm4.2''= | ||
This is the | |||
This gene was renamed to ocm4,2 from pvalb.2 on 7/2/2019 by KAB | |||
This gene is part of the ocm locus which has 3 ancestral genes. Placental mammals only retained one, but humans duplicated with a chomosomal break exactly at the ocm gene, resulting in two closely related genes named OCM1 and OCM2. KAB unilaterally renamed this more ancestral gene as ocm4 to facilitate proper orthology between genes of species which retain more paralogs from the original locus than human has. These proposed gene names are under review by HGNC. However, this gene is not properly homologous to OCM1 nor OCM2 in human. | |||
The ancestral locus, 5' to 3' is proposed to be OCM3 -> OCM4 -> OCM1 Note that xenopus massively duplicated the OCM4 paralogue. | |||
This gene should not be renamed unless instructed by HGNC | |||
=synteny and orthology notes= | |||
''X. tropicalis'' (as well as coelocanth and bony fish) have larger tandem arrays of OCM genes, specifically the OCM4 paralogues | |||
The gene symbols used for the tandem genes in this cluster are correct according to NCBI/Ref Seq (see discussion logged RSCOM-81). | |||
<CCZ1 <OCM1 <OCM4.6 <OCM4.5 <OCM4.4 <OCM4.3 <OCM4.2 <OCM4.1 <OCM3 LMTK2> | |||
NCBI REfseq tream agree with "Xenbase .. correctly names the gene adjacent to CCZ1 as OCM1 and ... properly name the gene adjacent to LMTK2 as OCM3". | |||
OCM3 has no orthologs in placental mammals but has orthologs in chicken NP_001007478.1, platypus XP_001512095.1, and opossum XP_007498332.1. | |||
The single OCM3 gene is related to a tandem cluster of genes Xenbase has named OCM4.1-OCM4.6. | |||
OCM4 has no orthologs in mammals but is orthologous to chicken XP_025011090.1. | |||
Latest revision as of 10:35, 6 June 2023
ocm4.2
This gene was renamed to ocm4,2 from pvalb.2 on 7/2/2019 by KAB
This gene is part of the ocm locus which has 3 ancestral genes. Placental mammals only retained one, but humans duplicated with a chomosomal break exactly at the ocm gene, resulting in two closely related genes named OCM1 and OCM2. KAB unilaterally renamed this more ancestral gene as ocm4 to facilitate proper orthology between genes of species which retain more paralogs from the original locus than human has. These proposed gene names are under review by HGNC. However, this gene is not properly homologous to OCM1 nor OCM2 in human.
The ancestral locus, 5' to 3' is proposed to be OCM3 -> OCM4 -> OCM1 Note that xenopus massively duplicated the OCM4 paralogue.
This gene should not be renamed unless instructed by HGNC
synteny and orthology notes
X. tropicalis (as well as coelocanth and bony fish) have larger tandem arrays of OCM genes, specifically the OCM4 paralogues
The gene symbols used for the tandem genes in this cluster are correct according to NCBI/Ref Seq (see discussion logged RSCOM-81).
<CCZ1 <OCM1 <OCM4.6 <OCM4.5 <OCM4.4 <OCM4.3 <OCM4.2 <OCM4.1 <OCM3 LMTK2>
NCBI REfseq tream agree with "Xenbase .. correctly names the gene adjacent to CCZ1 as OCM1 and ... properly name the gene adjacent to LMTK2 as OCM3".
OCM3 has no orthologs in placental mammals but has orthologs in chicken NP_001007478.1, platypus XP_001512095.1, and opossum XP_007498332.1.
The single OCM3 gene is related to a tandem cluster of genes Xenbase has named OCM4.1-OCM4.6.
OCM4 has no orthologs in mammals but is orthologous to chicken XP_025011090.1.