XB-FEAT-29084766: Difference between revisions
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QKRLVKIDKMAIIAIILNGVFVGIAILLGVLVFITYRKKSSSGDEENPPKKRKQKGKKEPSDESEESSSS | QKRLVKIDKMAIIAIILNGVFVGIAILLGVLVFITYRKKSSSGDEENPPKKRKQKGKKEPSDESEESSSS | ||
ESEESSSES | ESEESSSES | ||
BLAST of this Xtrop protein against ''X. laevis'' hits LOC101731164.L ( not represented on a gene page) , so the ID is still uncertain. | |||
=homology group analysis via EggNOGG v5= | =homology group analysis via EggNOGG v5= | ||
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Should this LOC# be called ''amica1''? | Should this LOC# be called ''amica1''? | ||
=nomenclature notes= | |||
11DEC23 | |||
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, can the Xtrop gene be called here ''jaml, junction adhesion molecule like''? | |||
=synteny= | =synteny= | ||
11DEC2023 | 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 | 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 it ( JAML) in the syntenic pattern- see table below (using mpzl2 as anchor). We think this is an error. | ||
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Latest revision as of 10:19, 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
BLAST of this Xtrop protein against X. laevis hits LOC101731164.L ( not represented on a gene page) , so the ID is still uncertain.
homology group analysis via EggNOGG v5
11DEC2023 LOC101730711 is an uncharacterized protein coding gene on Xtr.chr8, sitting among a cluster of similarly uncharacterized genes with 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 of this 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.
Should this LOC# be called amica1?
nomenclature notes
11DEC23
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, can the Xtrop gene be called here jaml, junction adhesion molecule like?
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 it ( JAML) in the syntenic pattern- see table below (using mpzl2 as anchor). We think this is an error.
| 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 |