XB-FEAT-22063928

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Revision as of 07:03, 10 October 2023 by Xenbase (talk | contribs) (Created page with "=''notch4''= This is the community wiki page for the gene ''notch4'' please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase. =gene nomenclature and annotation notes= In ''X. laevis'', on chromosome 8L, LOC121397048 is the gene next to ''tap2.L'' and we propose that represents a non-coding fragment of ''notch4''. This annotation was based on BLAST of notch4.S XM_041575228.1, which identified the loci n...")
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notch4

This is the community wiki page for the gene notch4 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.

gene nomenclature and annotation notes

In X. laevis, on chromosome 8L, LOC121397048 is the gene next to tap2.L and we propose that represents a non-coding fragment of notch4.

This annotation was based on BLAST of notch4.S XM_041575228.1, which identified the loci next to tap2.L and partially represented by lncRNA LOC121397048 as the X. laevis L version of notch4. David Web [NCBI refSeq] noted that the RNAseq data has a LOT of retained intron upstream of XR_005963385.1. He was not surprised that wasn't initially annotated as a coding gene, but he didn't try stitching the sequences together.

Synteny supports this conclusion as well.

  • In anurans (eg, X.laevis, X. tropicalis, Nano rana, Rana, and Bufo) synteny downstream of the NOTCH4 locus is conserved:

NOTCH4>...GPSM3<...PBX2>...RNF5<...AGPAT1>

  • but on the upstream side some of the genes seen in X. tropicalis are missing in other anurans or have an expansion of MHC-like genes inserted nearby:

PSMB9<...PSMB8>...TAP1<...TAP2>...HAUS3>...NOTCH4>

X.laevis chr8L seems to be missing HAUS3 and most of NOTCH4 while X. laevis 8S is missing PSMB8, TAP1, TAP2 though I'd have to do some work to certify the PSMB8/9 identities in S and L.

So, LOC121397048 name was updated to reflect that it is the notch4 ortholog. Xenbase and DW tentatively named it "notch4p.L, notch 4 L homeolog pseudogene" and promoted LOC121397048 to a tracked Gene [so it should show up in Entrez ID] and changed the locus type to 'pseudogene, transcribed'.

In X. tropicalis, there were 2x notch4 genes annotated in v10 assembly:

  • notch4.2 gene (GeneID: 101733027, XB-GENEPAGE-22063924)
  • notch4 GeneID: 100488695 XB-GENE-22063929.

we suspect NCBI kept it because it has a XenBase ID and XenBase keeps it because it has an NCBI ID.

NCBI merged notch4.2 GeneID: 101733027 XB-GENEPAGE-22063924 into notch4 GeneID: 100488695 XB-GENE-22063929.

Synteny

X.tropicalis chr8: psmb9 psmb8 tap1 LOC116406716 LOC100488859 GeneID:100488695:notch4 gpsm3 pbx2 rnf5 agpat1 egfl8


X.laevis chr8S: col11a2p1.S brd2.S mhc2a.S LOC108700221.S psmb9.S GeneID:108700568:notch4.S LOC108700223.S pbx2.S LOC121397630.S rnf5.S agpat1.S


X.laevis chr8L: LOC121397046.L LOC121397047.L LOC100037177.L mhc1a.L psmb8.L tap1.L tap2.L GeneID:121397048:notch4p.L LOC108698553.L pbx2.L rnf5.L


H.sapiens chr6: MIR6833 AGER PBX2 LOC124903764 GPSM3 GeneID:4855:NOTCH4 ABHD17AP8 LOC105379466 TP53TG3D TSBP1-AS1 LOC100507221

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