XB-FEAT-5740333: Difference between revisions
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Human symbol has changed for genepage ID: 5740333 From linc02867 to STUB1-DT, STUB1 divergent transcript . a psuedo gene in Humans. | Human symbol has changed for genepage ID: 5740333 From linc02867 to STUB1-DT, STUB1 divergent transcript . a psuedo gene in Humans. | ||
XB curators decided to keep this gene name as is, unchanged, as a lncRNA, | XB curators decided to keep this gene name as is, unchanged, as even though it is annotated/named as a non-coding lncRNA, it appears it to be functional protein coding gene in Xenopus. | ||
Do not change unless further compelling evidence is presented/published. | Note there is no gene in Xla.S | ||
Do not gene change name unless further compelling evidence is presented/published. | |||
=synteny maps= | =synteny maps= | ||
07JUNE2023 | |||
Xtr: '''linc02867'''< stub1> jmjd8<. XB5729975< LOC100487504[trim25]< | |||
Xla.L LOC108701691[trim25] jmjd8.L> stub1.L> '''loc440330.L(gene30787)''' rhbdl1.L< | |||
Xla.S XB5729975> stub1.S< rhbdl1.S< (note: not present in S) | |||
Human: ROT2> LOC#> RHBDL1> '''STUB-DT'''<. STUB1> JMJD8<. WDR24< | |||
Notes: | |||
Although Human STUB-DT1 and the ''Xenopus'' ''linc02867/loc440330'' are both flanked by STUVB1 and RHBDL1, these are not the same/orthologous genes. | |||
NCBI also doesnt identify eitehr Xenopus gene as orthols of STUB_DT1- mentioning on 3 orthog ( in hedgehog opossuma nd green anole). | |||
XB has therefore remove the human STUB-DT1 [Gene ID: 105371184] from this gene page. | |||
=DIOPT orthology group anlaysis= | |||
Using the below seq, DIOPT/EggNog tool matches this protein with >250 proteins from 235 species, including many fish mammals, with Xenopus [8364.ENSXETP00000061708], Danio rerio [7955.ENSDARP00000066582 zgc:112496]; Xiphophorus maculatus [8083.ENSXMAP00000019006]. | |||
Unfortiunately none of the close homologs are named in an informative manner, and no functional annotations are retrieved. | |||
Its a mystery!. | |||
Xtrop.linc02867 Entrez Gene: 100145131 | |||
>NP_001120112.1 uncharacterized protein LOC100145131 [Xenopus tropicalis] | |||
MAQNSGLFHSEDPAVWQKASDIYWDVIAAKGAKQKKLVSLDKWFQEELPPCIAARPHKHLTREELVKLME | |||
WKLTRGKFRPRLQQLVASNPDGAVETCTEKAFKLLPEVSAAINELCQLKGIGPATASAVLAAGAPELTAF | |||
MADEAVESIPGLTPVQYTLKHYLRYLEELRKKAAALSTEGSSEKWTPHQVELCLWAWEVARKLCPNLLGS | |||
QESGKIEERPKKKLKTK | |||
Latest revision as of 09:49, 7 June 2023
linc02867
This is the community wiki page for the gene linc02867 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase
nomenclature changes
12/05/2016
Human symbol has changed for genepage ID: 5740333 From loc440330 to loc105371184
10.18.2019
Human symbol has changed for Entrez Gene: 105371184. From LOC105371184 to linc02867
10.FEB.2021
Human symbol has changed for genepage ID: 5740333 From linc02867 to STUB1-DT, STUB1 divergent transcript . a psuedo gene in Humans.
XB curators decided to keep this gene name as is, unchanged, as even though it is annotated/named as a non-coding lncRNA, it appears it to be functional protein coding gene in Xenopus.
Note there is no gene in Xla.S
Do not gene change name unless further compelling evidence is presented/published.
synteny maps
07JUNE2023
Xtr: linc02867< stub1> jmjd8<. XB5729975< LOC100487504[trim25]<
Xla.L LOC108701691[trim25] jmjd8.L> stub1.L> loc440330.L(gene30787) rhbdl1.L<
Xla.S XB5729975> stub1.S< rhbdl1.S< (note: not present in S)
Human: ROT2> LOC#> RHBDL1> STUB-DT<. STUB1> JMJD8<. WDR24<
Notes: Although Human STUB-DT1 and the Xenopus linc02867/loc440330 are both flanked by STUVB1 and RHBDL1, these are not the same/orthologous genes.
NCBI also doesnt identify eitehr Xenopus gene as orthols of STUB_DT1- mentioning on 3 orthog ( in hedgehog opossuma nd green anole).
XB has therefore remove the human STUB-DT1 [Gene ID: 105371184] from this gene page.
DIOPT orthology group anlaysis
Using the below seq, DIOPT/EggNog tool matches this protein with >250 proteins from 235 species, including many fish mammals, with Xenopus [8364.ENSXETP00000061708], Danio rerio [7955.ENSDARP00000066582 zgc:112496]; Xiphophorus maculatus [8083.ENSXMAP00000019006].
Unfortiunately none of the close homologs are named in an informative manner, and no functional annotations are retrieved. Its a mystery!.
Xtrop.linc02867 Entrez Gene: 100145131
>NP_001120112.1 uncharacterized protein LOC100145131 [Xenopus tropicalis] MAQNSGLFHSEDPAVWQKASDIYWDVIAAKGAKQKKLVSLDKWFQEELPPCIAARPHKHLTREELVKLME WKLTRGKFRPRLQQLVASNPDGAVETCTEKAFKLLPEVSAAINELCQLKGIGPATASAVLAAGAPELTAF MADEAVESIPGLTPVQYTLKHYLRYLEELRKKAAALSTEGSSEKWTPHQVELCLWAWEVARKLCPNLLGS QESGKIEERPKKKLKTK