XB-FEAT-5734493: Difference between revisions
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The name of this gene (XB-GENEPAGE-5734493, NCBI GeneID:100379934, XP_002932289.1) was changed from ''rasef'' , ''ras and EF-hand domain-containing protein'' to '''''LOC100379934''' , '''ras and EF-hand domain-containing protein-like''','' as represents a rasef-like gene that was lost in the ancestor of mammals. The orthologs have been removed from this Xenbase gene page ( and placed on the true rasef gene page). | The name of this gene (XB-GENEPAGE-5734493, NCBI GeneID:100379934, XP_002932289.1) was changed from ''rasef'' , ''ras and EF-hand domain-containing protein'' to '''''LOC100379934''' , '''ras and EF-hand domain-containing protein-like''','' as represents a rasef-like gene that was lost in the ancestor of mammals. The orthologs have been removed from this Xenbase gene page ( and placed on the true rasef gene page). | ||
''LOC100379934/rasef-like'' is very similar protein-wise to the true ''rasef'', according to alignment in COBALT, and is flanked by different genes of course | ''LOC100379934/rasef-like'' is very similar protein-wise to the true ''rasef'', according to alignment in COBALT, and is flanked by different genes of course | ||
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Note that based on synteny (the conserved gene block), XB-GENE-1002558, NCBI GeneID: 780339, NP_001072877.1 represents the true ortholog to human RASEF (GeneID:158158), and accordingly it's name was changed from ''mgc147600'' to ''rasef''. | Note that based on synteny (the conserved gene block), XB-GENE-1002558, NCBI GeneID: 780339, NP_001072877.1 represents the true ortholog to human RASEF (GeneID:158158), and accordingly it's name was changed from ''mgc147600'' to ''rasef''. | ||
We have asked the HGNC to look at this gene to decide if it shoudl be called rasef-like or possible rasef2, a 2nd 'rasef' gene. Until then we will just keep the gene symbol as LOC100379934. | |||
=Synteny pattern= | =Synteny pattern= | ||
Revision as of 07:07, 14 September 2021
LOC100379934
This is the community wiki page for the gene LOC100379934 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
nomenclature changes
09/14/2021
The name of this gene (XB-GENEPAGE-5734493, NCBI GeneID:100379934, XP_002932289.1) was changed from rasef , ras and EF-hand domain-containing protein to LOC100379934 , ras and EF-hand domain-containing protein-like, as represents a rasef-like gene that was lost in the ancestor of mammals. The orthologs have been removed from this Xenbase gene page ( and placed on the true rasef gene page).
LOC100379934/rasef-like is very similar protein-wise to the true rasef, according to alignment in COBALT, and is flanked by different genes of course
in Gallus gallus (chicken) , the gene ( gene ID: 100858360 ) was already called 'ras and EF-hand domain-containing protein-like'.. and it has been indexed as an ortholog here.
Note that based on synteny (the conserved gene block), XB-GENE-1002558, NCBI GeneID: 780339, NP_001072877.1 represents the true ortholog to human RASEF (GeneID:158158), and accordingly it's name was changed from mgc147600 to rasef.
We have asked the HGNC to look at this gene to decide if it shoudl be called rasef-like or possible rasef2, a 2nd 'rasef' gene. Until then we will just keep the gene symbol as LOC100379934.
Synteny pattern
For this rasef-like gene, the synteny data in Latimeria chalumnae and non-mammalian tetrapods is generally:
PDIA3>...ELL3<...FKBP8-like>...SERF2>...RASEF-like<...ADAMTSL5-like>...SERINC4<...HYPK>.
In chondrichthyes and teleosts this synteny is somewhat conserved but the gene block is often shorter or re-arranged. The neighboring FKBP8-like and ADAMTSL5-like genes are also often lost (or possibly unannotated) in reptiles and mammals.
According to the v10 genome annotations, for X. tropicalis and X. laevis, Xenopus 'rasef-like' is on Chr3. Note that X. laevis has lost "serinc4. L and .S".
Xtrop: serf2 ... rasef-like ... adamtsl5 ... serinc4 ... hypk
Xlaevis.L: serf2.L ... rasef-like.L ... adamtsl5.L ... hypk.L
Xlaevis.S LOC# ... rasef-like.S... adamtsl5.S ... hypk.S (reversed order)
Human: SERF2 .. SERF2-C15orf63 ... SERINC4 ...HYPK
Gallus: : SERF2 ... LOC100858360 ... SERINC4 ...HYPK