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=


11DEC2023
11DEC2023
LOC101730711 is an uncharacterized protein coding gene on Xtr.chr8, among cluster of uncharacterized gens, carrying LOC##### symbols.
LOC101730711 is an uncharacterized protein coding gene on Xtr.chr8, sitting among a cluster of similarly uncharacterized genes with LOC##### symbols.


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The protein sequence o fthis uncharacterized protein matches 434 proteins in 96 species with high confidence,  most of which are named ''amica1''
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.
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=
=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 in in the systemic pattern- see table below (using mpzl2 as anchor).
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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=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''

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
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