XB-FEAT-5780435: Difference between revisions
imported>Xenbase →loc100145274: Updated nomenclature, replaced: unnamed → loc100145274 (2) |
imported>Xenbase |
||
| Line 1: | Line 1: | ||
= | = gtsf2 = | ||
This is the community wiki page for the gene '' | This is the community wiki page for the gene ''gtsf2'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase | ||
=nomenclature changes= | |||
following discussion is from David Webb at NCBI Refseq- subsequently, we renamed thi sgen to gtsf2. | |||
RSCOM-65 [https://ncbijira.ncbi.nlm.nih.gov/browse/RSCOM-65?jql=project%20%3D%20RSCOM%20AND%20status%20in%20(Open%2C%20%22In%20Progress%22)%20AND%20text%20~%20xenopus%20ORDER%20BY%20created%20DESC] | |||
Hi XenBase, CGNC, RGD, VGNC: | |||
All of you have properly named the GTSF1 gene but the tandem GTSF2 gene has gone unnamed because humans lack it. I'll create subtasks for each nomenclature authority. | |||
Here's the messy evidence: | |||
Most tetrapods have tandem gametocyte specific factor (GTSF) genes situated between NCKAP1L and ITGA5. | |||
Primates have lost one of these GTSF genes. In non-primate mammals and amphibians you have PPP1R1A> <PDE1B <NCKAP1L GTSF2> GTSF1> ITGA5> ZNF385A> GPR84>. The coelocanth assembly is a mess but otherwise this gene block isn't found outside of tetrapods (and I searched for the genes on both sides of the GTSF genes). | |||
In mouse, GTSF1 is GeneID: 74174; MGI:1921424 and GTSF2 is GeneID: 223927; MGI:2652828. | |||
Reptiles usually conserve the tetrapod gene synteny but an array of keratin genes is sometimes inserted in the region and the assemblies are frequently fragmented. Lizards typically have PPP1R1A> <PDE1B <NCKAP1L GTSF2> GTSF1> ITGA5> <keratins>. Alligator sinensis has the typical tetrapod synteny. | |||
Birds appear to have partially conserved this block: PPP1R1A> <PDE1B <NCKAP1L GTSF2> but have moved the GTSF1 gene to a novel chr location at <many keratins> GTSF1> <GOSR2 <WNT9B WNT3>. In most all other tetrapods this gene block is <ITGB3 RPRML> <GOSR2 <WNT9B WNT3>. (Note how ITGA5, ITGB3, and the keratins may have facilitated the chromosome rearrangement). | |||
Consistent with CGNC:753; GeneID:771059 being GTSF1 and CGNC:67256; GeneID:101747763 being GTSF2, GeneID: 771059 has higher identity to human GTSF1 than does GeneID: 101747763 (55% vs 46% ID) while GeneID: 101747763 shares one-sided synteny with mammalian GTSF2 genes. BLASTp of chicken vs mouse also shows GeneID: 771059 having significantly higher identity to the mouse GTSF1 protein. | |||
X. tropicalis has tandem genes XB-GENE-5878704 (GeneID:100036720; GTSF1) and XB-GENE-5780436 (GeneID:100145274; XB5780435). I think XB-GENE-5780436 should be named GTSF2 as these genes are syntenic with the mouse GTSF2 and GTSF1 genes. | |||
G. gallus has partially broken this synteny but I think CGNC:67256; GeneID:101747763 should be renamed GTSF2 and CGNC:753; GeneID:771059 can remain GTSF1. | |||
Revision as of 13:38, 6 July 2020
gtsf2
This is the community wiki page for the gene gtsf2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature changes
following discussion is from David Webb at NCBI Refseq- subsequently, we renamed thi sgen to gtsf2.
RSCOM-65 [1]
Hi XenBase, CGNC, RGD, VGNC: All of you have properly named the GTSF1 gene but the tandem GTSF2 gene has gone unnamed because humans lack it. I'll create subtasks for each nomenclature authority.
Here's the messy evidence:
Most tetrapods have tandem gametocyte specific factor (GTSF) genes situated between NCKAP1L and ITGA5.
Primates have lost one of these GTSF genes. In non-primate mammals and amphibians you have PPP1R1A> <PDE1B <NCKAP1L GTSF2> GTSF1> ITGA5> ZNF385A> GPR84>. The coelocanth assembly is a mess but otherwise this gene block isn't found outside of tetrapods (and I searched for the genes on both sides of the GTSF genes).
In mouse, GTSF1 is GeneID: 74174; MGI:1921424 and GTSF2 is GeneID: 223927; MGI:2652828.
Reptiles usually conserve the tetrapod gene synteny but an array of keratin genes is sometimes inserted in the region and the assemblies are frequently fragmented. Lizards typically have PPP1R1A> <PDE1B <NCKAP1L GTSF2> GTSF1> ITGA5> <keratins>. Alligator sinensis has the typical tetrapod synteny.
Birds appear to have partially conserved this block: PPP1R1A> <PDE1B <NCKAP1L GTSF2> but have moved the GTSF1 gene to a novel chr location at <many keratins> GTSF1> <GOSR2 <WNT9B WNT3>. In most all other tetrapods this gene block is <ITGB3 RPRML> <GOSR2 <WNT9B WNT3>. (Note how ITGA5, ITGB3, and the keratins may have facilitated the chromosome rearrangement).
Consistent with CGNC:753; GeneID:771059 being GTSF1 and CGNC:67256; GeneID:101747763 being GTSF2, GeneID: 771059 has higher identity to human GTSF1 than does GeneID: 101747763 (55% vs 46% ID) while GeneID: 101747763 shares one-sided synteny with mammalian GTSF2 genes. BLASTp of chicken vs mouse also shows GeneID: 771059 having significantly higher identity to the mouse GTSF1 protein.
X. tropicalis has tandem genes XB-GENE-5878704 (GeneID:100036720; GTSF1) and XB-GENE-5780436 (GeneID:100145274; XB5780435). I think XB-GENE-5780436 should be named GTSF2 as these genes are syntenic with the mouse GTSF2 and GTSF1 genes.
G. gallus has partially broken this synteny but I think CGNC:67256; GeneID:101747763 should be renamed GTSF2 and CGNC:753; GeneID:771059 can remain GTSF1.