XB-FEAT-5833500: Difference between revisions
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The ancestral locus, 5' to 3' is proposed to be OCM3 -> OCM4 -> OCM1 | The ancestral locus, 5' to 3' is proposed to be OCM3 -> OCM4 -> OCM1 | ||
= | =synteny notes= | ||
X. tropicalis (as well as coelocanth and bony fish) have larger tandem arrays of OCM genes, specifically the OCM4 paralogues | ''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). | The gene symbols used for the tandem genes in this cluster are correct according to NCBI/Ref Seq (see discussion logged RSCOM-81). | ||
Revision as of 10:30, 6 June 2023
ocm3
This is the community wiki page for the gene ocm3 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenlcature changes
This gene was renamed to ocm3 from pvalb on 7/1/2019 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 ocm3 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 duplicated the OCM4 paralogue.
This gene should not be renamed unless instructed by HGNC
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 ocm1 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
synteny 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.