XB-FEAT-29072457: Difference between revisions
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=Synteny patterns= | =Synteny patterns= | ||
ANLN orthologs: | |||
Xtrop.Chr6: ''elmo1> aoah> '''LOC100491625'''< matcap2> eepd1<'' | |||
Xla.Chr6L: ''elmo1.L> aoah.L> '''anln.L'''< matcap2.L> eepd1.L<'' | |||
spinytoad.chr5: ''eepd1> LOC> '''anln'''> aoah< elmo1<'' | |||
Human.Chr7: MATCAP2<* '''ANLN'''>* [ENHACERS] AOAH< NPM1P18> ELMO1< | |||
Chick.Chr2: elmo1> aoah> *'''anln'''< * kia0895> eepd1< septin 7< | |||
Note that ''anln'' in fish doesn't follow the syntentic pattern: | |||
Danio.Chr19: rnf19b< ak2< *'''anln'''< *ptp2a2b< col18a2 | |||
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synteny: | synteny: | ||
Xtrop.chr4: ''matcap1< exoc3L1< '''anln2'''< tmem208< usp1> elmo3> e2f4<'' | |||
Xla.chr4L: ''exoc3l1.L< '''LOC108714167'''< tmem208.L< usp1.L> elmo3.L< e2f4.L<'' | |||
Xla.Chr4S:(rv) ''matcap1.S< '''LOC121393288'''> tmem208.S< usp1.S> e2f4.S>'' | |||
whereas in mammals..... | whereas in mammals..... | ||
Human.CHR16: MATCAP1< EXOC3L1< LOC[ENHANCER]> E2F4> ELMO3> FBXL9P< TMEM208> FHOD1< | |||
Mouse.CHR8: Hsf4> Nol3> Matcap1< Exoc3l< E2f4> Elmo3> Fbx19< Tmem208> Fhod1< | |||
Latest revision as of 08:16, 5 May 2023
anln2
This is the community wiki page for the gene anln2 please feel free to add any information that is relevant to this gene that is not already captured elsewhere in Xenbase.
gene annotation, nomenclature and synteny
Two different genes were annotated as anillin/anillin actin binding protein, 'anln' in Xenopus v10 genomes
1) Xtr.anln (GeneID:100491625; ENSXETG00000000343) and Xla.anln.L (GeneID:398569) genes on Chr6/6L, with synteny conserved in mammals, frogs, chicken.
Based on synteny with mammals & chick ( see below) these are considered the true ANLN orthologs, and thus should keep the anln gene symbol.
05MAY2023
Zfin and Xenbase agreed to the ANLN2 nomenclature, then made the needed updates:
1. Xenbase ANLN gene page XB-GENEPAGE-489406 should remove Xtr GeneID:100329114 (ENSXETG00000039411 since that's the ANLN2 gene and add Xtr GeneID:100491625 (ENSXETG00000000343). Xla.L Gene ID: 398569 should remain on XB-GENEPAGE-489406 as ANLN. I couldn't find an Xla.S ortholog. The gene description could be 'anillin, actin binding protein' as in zebrafish and human.
2. create a Xenbase gene page for ANLN2/'anillin, actin binding protein 2' [XB-GENEPAGE-29072457] with Xtr GeneID:100329114 (ENSXETG00000039411) and Xla.L GeneID: 108714167 (ENSXLAG00005012375).
Note that Xla.S GeneID: 121393288 is the ANLN2 ortholog as it shares synteny but oddly is a single coding exon and was probably retrotransposed into an intron of the USP1 gene. This gene still needs to be added to XB-GENEPAGE-29072457.
3. Zfin ZDB-GENE-030131-4486 (GeneID: 562517, ANLN) is fine. ZDB-GENE-060503-826 (GeneID: 559353, ENSDARG00000088130, si:dkey-30c15.10) should be renamed as ANLN2/'anillin, actin binding protein 2'.
Synteny patterns
ANLN orthologs:
Xtrop.Chr6: elmo1> aoah> LOC100491625< matcap2> eepd1<
Xla.Chr6L: elmo1.L> aoah.L> anln.L< matcap2.L> eepd1.L<
spinytoad.chr5: eepd1> LOC> anln> aoah< elmo1<
Human.Chr7: MATCAP2<* ANLN>* [ENHACERS] AOAH< NPM1P18> ELMO1<
Chick.Chr2: elmo1> aoah> *anln< * kia0895> eepd1< septin 7<
Note that anln in fish doesn't follow the syntentic pattern:
Danio.Chr19: rnf19b< ak2< *anln< *ptp2a2b< col18a2
2) Xtr.anln2 (GeneID:100329114; ENSXETG00000039411) and Xla.anln2.L (GeneID:108714167) are on chr 4/4L, where synteny is conserved acrosss Xenopus, other frogs and fishes, but seems it is missing/lost in mammals and birds ( according to Genomicus) .
A new gene pages for the Chr4 genes and call them anln2 with NCBI RefSeq team and HGNC approval.
synteny:
Xtrop.chr4: matcap1< exoc3L1< anln2< tmem208< usp1> elmo3> e2f4<
Xla.chr4L: exoc3l1.L< LOC108714167< tmem208.L< usp1.L> elmo3.L< e2f4.L<
Xla.Chr4S:(rv) matcap1.S< LOC121393288> tmem208.S< usp1.S> e2f4.S>
whereas in mammals.....
Human.CHR16: MATCAP1< EXOC3L1< LOC[ENHANCER]> E2F4> ELMO3> FBXL9P< TMEM208> FHOD1<
Mouse.CHR8: Hsf4> Nol3> Matcap1< Exoc3l< E2f4> Elmo3> Fbx19< Tmem208> Fhod1<