XB-FEAT-1000743: Difference between revisions
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This naming is supported by synteny, and this research article: Ochi et al 2017 ''Co-accumulation of cis-regulatory and coding mutations during the pseudogenization of the Xenopus laevis homoeologs six6.L and six6.S.'' Dev Biol 2017 Jul 01;4271:84-92. PubMed ID: '''28501477''' . | This naming is supported by synteny, and this research article: Ochi et al 2017 ''Co-accumulation of cis-regulatory and coding mutations during the pseudogenization of the Xenopus laevis homoeologs six6.L and six6.S.'' Dev Biol 2017 Jul 01;4271:84-92. PubMed ID: '''28501477''' . | ||
Note that Gene models for ''X. laevis c8h14orf39 /c14orf39/ LOC100486324'' were absent in the v9 genome assemblies but are present in | Note that Gene models for ''X. laevis c8h14orf39 /c14orf39/ LOC100486324'' were absent in the v9 genome assemblies but are present in the v10 assembly. See synteny below. | ||
=synteny map= | =synteny map= | ||
Note that ''six6os1''( previously called ''c8h14orf39'') is up/downstream from ''six4''''six1'' and ''six6'' (the anchor with gene IDs)in ''Xenopus''. | Note that ''six6os1''( previously called ''c8h14orf39'') is up/downstream from ''six4'' ,''six1'' and ''six6'' (the anchor with gene IDs) in ''Xenopus''. | ||
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Latest revision as of 09:41, 18 March 2024
six6os1
This is the community wiki page for the gene six6os1 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
05DEC2022
HGNC and NCBIs RefSeq team have recently renamed all non-human open reading frame (ORF) genes. The new Xenopus gene symbol syntax reflects the orthology to the human gene while starting with a prefix indictating location of the ORF on the Xenopus chromosome, i.e., the Xenopus chromosome number (c#), then 'h#' for the human chromosome number, then the same human 'orf #'. Old human 'c'orf' gene symbols are recorded as synonyms.
25MAY2023
Gene symbol changed from c14orf39 /.L/.S to c8h14orf39 and name changed from "chromosome 14 open reading frame 39" to "chromosome 8 C14orf39 homolog", according to new c#h##orf# naming rules.
c14orf39 added as a synonym to this gene.
30Nov2023
Xenopus gene name changed from c8h14orf39, "chromosome 8 C14orf39 homolog" to six6os1, six6 opposite strand transcript 1 following the rat ortholg name, and our need to give protein coding genes more meaningful names.
This naming is supported by synteny, and this research article: Ochi et al 2017 Co-accumulation of cis-regulatory and coding mutations during the pseudogenization of the Xenopus laevis homoeologs six6.L and six6.S. Dev Biol 2017 Jul 01;4271:84-92. PubMed ID: 28501477 .
Note that Gene models for X. laevis c8h14orf39 /c14orf39/ LOC100486324 were absent in the v9 genome assemblies but are present in the v10 assembly. See synteny below.
synteny map
Note that six6os1( previously called c8h14orf39) is up/downstream from six4 ,six1 and six6 (the anchor with gene IDs) in Xenopus.
| Species | Chromosome | < 5 | < 4 | < 3 | < 2 | < 1 | Gene of Interest | > 1 | > 2 | > 3 | > 4 | > 5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| X.tropicalis | chr8 | slc38a6 | trmt5 | mnat1 | six4 | six1 | GeneID:100101705;six6; | c8h14orf39 | ppm1a | dhrs7 | pcnx4 | lrrc9 |
| X.laevis | chr8S | jkamp.S | rtn1.S | dhrs7.S | ppm1a.S | LOC108699751.S | GeneID:373784;six6.S; | six1.S | six4.S | mnat1.S | hif1a.S | kcnh5.S |
| X.laevis | chr8L | slc38a6.L | trmt5.L | mnat1.L | six4.L | six1.L | GeneID:398128;six6.L; | LOC121396872 | ppm1a.L | dhrs7.L | pcnx4.L | lrrc9.L |
| M.musculus | Chr12 | dhrs7 | ppm1a | Gm33785 | Gm40441 | 4930447C04Rik | GeneID:20476; Six6 | six1 | MIR9718 | six4 | mnat1 | Gm23910 |
| H.sapiens | Chr14 | LINC02322 | RBM8B | GNRHR2P1 | C14orf39 | SALL4P7 | GeneID:4990; SIX6 | VN1R59P | RPL37P5 | RPS15AP4 | SALRNA1 | six1 |