XB-FEAT-5734493

rasef2

This is the community wiki page for the gene rasef2 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, CGNC, and ZFIN are okay with naming the RASEF-like gene, 'RASEF2','RAS and EF-hand domain containing 2'?

This RASEF-like gene corresponds to:

Xtr GeneID:100379934 XB-GENE-5734494

Gg GeneID:100858360 CGNC:64721 (LOC100858360)

Dr Gene ID: 572256 ZFIN:ZDB-GENE-070424-92 (zgc:162879)

28APRIL2023

Xenopus gene symbol changed to LOC100379934 to rasefl

12SEPT2023 After review by NCBI RefSeq team and Xenbase, and based on BLASTp and synteny:

Xenopus gene symbol was changed from rasefl to rasef2

Xenopus gene name was changed from RAS and EF-hand domain containing like to RAS and EF-hand domain containing 2

Notes from David Webb:

Xenopus GeneID: 100379934 (XB-GENE-5734494) is clearly the closest paralog to the vertebrate RASEF gene (eg,human RASEF GeneID:158158 or zebrafish GeneID: 570731, ZDB-GENE-081105-157) and, since it contains the same domains as the RASEF protein, RASEF2 / 'RAS and EF-hand domain containing 2' seems appropriate.

Lamprey appears to have had a single RASEF gene which was duplicated in gnathostomes into RASEF and RASEF2 and then RASEF2 was lost in amniotes. This RASEF2 gene is tail-to-tail with SERF2 in chondrichthyes and through teleosts and amphibians.

I found no [prior] references to a RASEF2 gene online, [so we are free to use it here].

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".

X. trop: serf2 ... rasef-like ... adamtsl5 ... serinc4 ... hypk

X. laevis.L: serf2.L ... rasef-like.L ... adamtsl5.L ... hypk.L

X. laevis.S LOC# ... rasef-like.S... adamtsl5.S ... hypk.S (reversed order)

Human: SERF2 .. SERF2-C15orf63 ... SERINC4 ...HYPK

Gallus: : SERF2 ... LOC100858360 ... SERINC4 ...HYPK

David Webb commented on RSCOM-162:

---

The RASEF-like protein has the same domain structure as RASEF (N-terminal EF-hand-7 domain, central SMC domain, C-terminal P-loop NTPase domain) and the synteny is conserved in gnathostomes.

The RASEF gene generally resides in tetrapods at:

TLE1<...RASEF<...FRMD3<...IDNK>...UBQLN1<...GKAP1<...KIF27<

The RASEF-like gene[ now called RASEF2] resides at:

thorny skate ...ELL3?<...FKBP8-like>...SERF2>...RASEF-like<...

D. rerio ...ELL3?<...FKBP8-like>...SERF2>...RASEF-like<...SEMA4BA<...ZNF10A>

gar, reedfish ...ELL3?<...FKBP8-like>...SERF2>...RASEF-like<...ERAP1<...SEMA4B<...ZNF10>

coelacanth PDIA3>...ELL3<...FKBP8-like>...SERF2>...RASEF-like<...loc<...ADAMTSL5>...SERINC4<...HYPK>...MFAP1<

amphibians PDIA3>...ELL3<...FKBP8-like>...SERF2>...RASEF-like<...ADAMTSL5>...SERINC4<...HYPK>...MFAP1<

birds & reptiles are variable but ancestral state seems to be PDIA3>...ELL3<...FKBP8-like>...SERF2>...RASEF-like<...SERINC4<...HYPK>...MFAP1<

chicken PDIA3>...SERF2>...RASEF-like<...SERINC4<...HYPK>...MFAP1<

mammals (in addition to RASEF2, have lost or pseudogenized FKBP8-like gene and ADAMTS-like gene) PDIA3>...ELL3<...FKBP-pseudogene?>...SERF2>...SERINC4<...HYPK>...MFAP1<