XB-FEAT-29084766: Difference between revisions
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Strangely, NCBI has the ''X.trop mpzl3'' gene listed as an orthology of human JAML, even though the structure/architecture of this protein is completely different, but it is very close to in in the | Strangely, NCBI has the ''X.trop mpzl3'' gene listed as an orthology of human JAML, even though the structure/architecture of this protein is completely different, but it is very close to in in the syntenic pattern- see table below (using mpzl2 as anchor). | ||
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Revision as of 09:25, 11 December 2023
protein
uncharacterized protein LOC101730711 [Xenopus tropicalis]
NCBI Reference Sequence: XP_017952313.2
>XP_017952313.2 uncharacterized protein LOC101730711 [Xenopus tropicalis] MCHILIFILLFLFLFQRKICEGRGRLSCPAVMGPARLHPFIILLGLFHLFLSSTSAVKVENFTLFEEKLK LEAHTANMIPCVFHTRRRLNPLRVQLEWGKMDKEGYVPLIHLDGNHVRKAAADFGDKYQLFIPQVSQGNC SLVINPMDIADSGTYQVRLRILGKLYEPVPSIEIQVVDQRKVESRAWGKKKTTVPPTTIATVPPGFVDDV QKRLVKIDKMAIIAIILNGVFVGIAILLGVLVFITYRKKSSSGDEENPPKKRKQKGKKEPSDESEESSSS ESEESSSES
homology group analysis via EggNOGG v5
11DEC2023 LOC101730711 is an uncharacterized protein coding gene on Xtr.chr8, among cluster of uncharacterized gens, carrying LOC##### symbols.
| Species | Chromosome | < 5 | < 4 | < 3 | < 2 | < 1 | Gene of Interest | > 1 | > 2 | > 3 | > 4 | > 5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| X.tropicalis | chr8 | cfap45 | nlrp4 | LOC116406898 | LOC116406897 | LOC100486737 | GeneID:101730711;LOC101730711; | LOC100488807 | LOC100488643 | LOC101730590 | LOC116406952 | LOC100491706 |
The protein sequence o fthis uncharacterized protein matches 434 proteins in 96 species with high confidence, most of which are named amica1
the protein has 1 or more Immunoglobulin V-set domain(s) and has assigned monocyte extravasation as a major molecular function.
synteny
11DEC2023 Strangely, NCBI has the X.trop mpzl3 gene listed as an orthology of human JAML, even though the structure/architecture of this protein is completely different, but it is very close to in in the syntenic pattern- see table below (using mpzl2 as anchor).
| Species | Chromosome | < 5 | < 4 | < 3 | < 2 | < 1 | Gene of Interest | > 1 | > 2 | > 3 | > 4 | > 5 |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| X.tropicalis | chr7 | atp5mg | ube4a | LOC116412324 | cd3g | cd3e | GeneID:549209;mpzl2; | mpzl3 | scn2b | scn4b | tmprss4 | smim35 |
| X.laevis | chr7L | vps11.L | kmt2a.L | atp5mg.L | ube4a.L | cd3e.L | GeneID:446705;mpzl2.L; | mpzl3.L | scn2b.L | LOC121395544 | scn4b.L | tmprss4.L |
| H.sapiens | Chr11 | scn4b | scn2b | JAML | HSPE1P18 | mpzl3 | GeneID:10205; MPZL2 | cd3e | CD3D | cd3g | ube4a | LOC100131626 |
| M.musculus | chr9 | ube4a | Gm19121 | cd3g | CD3D | cd3e | GeneID:14012; Mpzl2 | mpzl3 | JAML | Gm10684 | scn2b | scn4b |
nomenclature changes
AMICA1, is now called JAML junction adhesion molecule like in Homo sapiens (human) (Gene ID: 120425) which was updated on NCBI on 23-Nov-2023
Based on these preliminary analysis, the Xtrop gene is here jaml, junction adhesion molecule like