Latest revision as of 09:25, 5 May 2023

anln

This is the community wiki page for the gene anln 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 mamals & chick, these are considered the true ANLN orthologs, and thus should keep the anln gene symbol.

Synteny patterns

Xtropchr6: elmo1> aoah> LOC100491625< matcap2> eepd1<

Xla.Chr6L: elmo1.L> aoah.L> anln.L< matcap2.L> eepd1.L<

spinytoadchr5: eepd1> LOC> anln> aoah< elmo1<

HumanChr7: MATCAP2<* ANLN>* [ENHACERS] AOAH< NPM1P18> ELMO1<

ChickChr2: elmo1> aoah> *anln< * kia0895> eepd1< septin 7<

note that anln in fish doesn't follow the syntentic pattern:

DanioChr19: rnf19b< ak2< *anln< *ptp2a2b< col18a2

2) Xtr.anln (GeneID:100329114; ENSXETG00000039411) and Xla.anln.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) .

Xtropchr4: matcap1< exoc3L1< anln< tmem208< usp1> elmo3> e2f4<

Xlachr4L: exoc3l1.L< LOC108714167< tmem208.L< usp1.L> elmo3.L< e2f4.L<

XlaChr4S:(rv) matcap1.S< LOC121393288> tmem208.S< usp1.S> e2f4.S>

FULL synteny patterns fro ANLN and ANLN2 orthologs

from NCBI refSeq David Webb

01MAY2023

True ANLN ortholog synteny:

Xtrop XP_002939460.1 GeneID:100491625

SEPTIN7> EEPD1> MATCAP2> *ANLN*> AOAH< ELMO1<

Xla.L NP_001082562.1 Gene ID: 398569

SEPTIN7> EEPD1> MATCAP2> *ANLN.L*> AOAH< ELMO1<

Bufo bufo NOTE: matcap2 flip

SEPTIN7> EEPD1> MATCAP2> *ANLN*> AOAH< ELMO1<

Human NP_061155.2

SEPTIN7> EEPD1> MATCAP2< *ANLN*> AOAH< ELMO1<

Chick XP_015137168.2

SEPTIN7> EEPD1> MATCAP2< *ANLN*> AOAH< ELMO1<

Latimeria chalumnae XP_014347707.1 many assembly gaps

SEPTIN7> EEPD1> MATCAP2< *ANLN*> ELMO1<//

reedfish, gar XP_015213014.1

SEPTIN7A> EEPD1> MATCAP2< *ANLN*> ELMO1< RP9< C18orf21<

Dr NP_001096146.2 GeneID: 562517

COL8A2> PTP4A2B> *ANLN*> AK2> RNF19B> NDUFS5>

Great White Shark XP_041040850.1

EEPD1> MATCAP2> *ANLN*> ELMO1< RP9< GGCT> OSBPL10>

lamprey XP_032816504.1 /*ANLN*/

ANLN-like/ANLN2 ortholog synteny:

Xtrop XP_012817087.2 GeneID:100329114

E2F4> ELMO3> USP1< TMEM208> *anln*> EXOC3L1> MATCAP1>

Xla.L XP_041446205.1 Gene ID: 108714167

E2F4> ELMO3> USP1< TMEM208> *anln.L*> EXOC3L1> prkcd< MATCAP1>

Xla.S possibly GeneID: 121393288 XP_041417179.1 Note single coding exon residing in intron of USP1. E2F4> USP1< *anln.S*< TMEM208> MATCAP1pseudo>

Rhinatrema E2F4> ELMO3> LRRC29< TMEM208> *anln*> EXOC3L1> MATCAP1> eepd1?<

Human

MATCAP1< EXOC3L1< LOC> E2F4> ELMO3> FBXL9P< TMEM208> FHOD1<

Mouse

HSF4> NOL3> MATCAP1< EXOC3L1< E2F4> ELMO3> FBX19< TMEM208> FHOD1<

Monodelphis

HSF4> NOL3> MATCAP1< EXOC3L1< E2F4> ELMO3> LRRC29< TMEM208> FHOD1<

echidna

NOL3> MATCAP1< EXOC3L1< E2F4> ELMO3> LRRC29< TMEM208> FHOD1<

Chelonia

CTRL< EXOC3L1< E2F4> ELMO3> LRRC29< TMEM208> MATCAP1< LCAT<

Komodo dragon

CTRL< EXOC3L1< E2F4> ELMO3> LRRC29< TMEM208> ZDHHC1>

Gallus

CTRL< EXOC3L1< E2F4> ELMO3> LRRC29< TMEM208> MATCAP1< LCAT<

lungfish XP_043937366.1

RALYL> E2F4> ELMO3> LRRC29< TRIM71> TMEM208> *anln*> AHR> EXOC3>

Latimeria chalumnae XP_005988024.1

TMEM208> *anln*> AHR> EXOC3L1> MATCAP1> EEPD1<

gar XP_015223404.1

CCL#< SEPT7-like> *anln*> AHR> EXOC3L1> TRIM?<

Dr si:dkey-30c15.10 ZDB-GENE-060503-826 XP_009291711.1

LOC> CCDC79< PDP2> *anln*> CDH1-like> LOC> SYT1B<

/E2F4> ELMO3> LRRC29> TRIM#</

/EXOC3L1/

/AHR1A/ /AHR2> AHR1B>/

Great White Shark XP_041047520.1

EEPD1> MATCAP1< *anln*> AHR> EXOC3L1> TMEM208> TRIM71> LRRC29> ELMO3< E2F4<

skate XP_032891944.1

EEPD1> MATCAP1< *anln*> EXOC3L1> TMEM208> TRIM71> LRRC29> ELMO3< E2F4<

lamprey XP_032827074.1

//MATCAP1< *anln*> MRPL3< CEP192> LDLRAD4>

whereas in mammals.....

Humanchr16: MATCAP1< EXOC3L1< LOC[ENHANCER]> E2F4> ELMO3> FBXL9P< TMEM208> FHOD1<

MouseCHR8: hsf4> nol3> matcap1< exoc3l< e2f4> elmo3> fbx19< tmem208> fhod1<

actions

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'.

XB-FEAT-489406: Difference between revisions