RetrogeneDB ID: retro_ogar_2196

Retrocopy location

• Organism: Bushbaby (Otolemur garnettii)
• Coordinates: GL873600.1:5700839..5701859(-)
• Located in intron of: ENSOGAG00000016085

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: SUCLA2
• Ensembl ID: ENSOGAG00000007452
• Aliases: None
• Description: succinate-CoA ligase, ADP-forming, beta subunit [Source:HGNC Symbol;Acc:11448]

Sequence

>retro_ogar_2196
GCAACCTCTATGATTTACGGTCAACTGTTGGTAACCACTACCATTCAGAGCCACAGACCCCAGACAATGCTGCAGGCTGC
TGTCCAGGTTCTGGGAAGTTCTGGATTCTTTAATAATCATGGACTGCAAGTATAGCAACAACAGCAAAGAAATCTCTCAC
TACATGAATATGAGTACATGCATATGGAATTGTGGCAAGAAGCTAGCATCTCCATTCCCAGAGGATTTGCGGCAAAGTCA
CCAGAGGAAGCTTATGCAAATGCCAAAAAGTTAGGTTCAAAAGATGTTGTGATAAAGGCACAGGTTTTAGCCGGTGGTAG
AGGAAAAGGAATATTTGAAAGCAGTCTGAAAGGGGGAATGAAGATAGTTTTCTCTCCAGAACAAGCAAAAGCTGTTTCCT
CACAAATGATTGGGAAAAAATTGTTTACCATGCAAACAGGAGAAAAGGGTGGAATATGCAATCAAGTATTGGTCTGTGAG
CAAAAATATCCCAGGAAGAATACAACTTTGCAAATAACAATGGAAAGGTCATTTTGATGTCCCGTGTTAATAGGAAGTTC
TCAAGGTGGTGTCAACTTTGAAGAAGTTGCTGTTGAGACCCCCCAAGGCAATAGTTAAAGAACCTGTTGATATTTTAGAA
GGCATCAAGAAGGAACAAGCTCTCTGGCTTGCACAGAAGATGGGATTTCTATCTAATACAGTGGATTCCGCTGCAAATAA
AACATGGTCAAGTTTTACCTTTTTCTGAAATACAATGCAACCATGGTAAAAAATAAATCCGATGGTAGAAGATTCAGATG
GAGTTGTGCTCTGTATGGATGCAAGATCAATTTTGATTCTAATTCAGCCTACCACCAGAAGGAAATCTTTGCTCTACAGG
ACTGGACCCAGGAAGATAAAAGGGACAAAGATGCAGCTAAGGCAGATCTCAACTACATTGGCCTCAATGGAAATACAGGC
TGTCTAATAAATGATGCTGGTTTGGCTATTGCCACAATGGATCTAATATGGATGGTGGGA

Alignment

ORF - retro_ogar_2196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.74 %
• Parental protein coverage: 73. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  AASMIYGRLLVAAAFRSNRPRTALQAAAQVLGSSGLFNNHGLQVQQQQQRNLSLHEY--MSMELLQEAGV
          A.SMIYG.LLV.....S.RP.T.LQAA.QVLGSSG.FNNHGLQV.QQQQRNLSLHEY..M.MEL.QEA..
Retrocopy ATSMIYGQLLVTTTIQSHRPQTMLQAAVQVLGSSGFFNNHGLQV*QQQQRNLSLHEYEYMHMELWQEASI

Parental  SIPKGFVAKSPDEAYAIAKKLGSKDVVIKAQVLAGGRGKGTFESGLKGGVKIVFSPEEAKAVSSQMIGKK
          SIP.GF.AKSP.EAYA.AKKLGSKDVVIKAQVLAGGRGKG.FES.LKGG.KIVFSPE.AKAVSSQMIGKK
Retrocopy SIPRGFAAKSPEEAYANAKKLGSKDVVIKAQVLAGGRGKGIFESSLKGGMKIVFSPEQAKAVSSQMIGKK

Parental  LITKQTGEKGRICNQVLVCERRYPRREYYFAITMERSFQGPVLIGSSQGGVNIEDVAAETPE-AIVKEPI
          L.T.QTGEKG.ICNQVLVCE..YPR......ITMERSF..PVLIGSSQGGVN.E.VA.ETP..AIVKEP.
Retrocopy LFTMQTGEKGGICNQVLVCEQKYPRKNTTLQITMERSF*CPVLIGSSQGGVNFEEVAVETPQ>AIVKEPV

Parental  DIVEGIKKEQALRLAQNMGFPSNIVDSAAENM-VKLYDLFLKYDATMV-EINPMIEDSDGAVLCMDA-KI
          DI.EGIKKEQAL.LAQ.MGF.SN.VDSAA.........LFLKY.ATMV..INPM.EDSDG.VLCMDA.KI
Retrocopy DILEGIKKEQALWLAQKMGFLSNTVDSAANKT<MVKFYLFLKYNATMV>KINPMVEDSDGVVLCMDA<KI

Parental  NFDANSAFRQKEIFALQDWTQEDERDKDAAKAHLNYIGLDGNIGCLVNGAGLAMATMDIIKLHG
          NFD.NSA..QKEIFALQDWTQED.RDKDAAKA.LNYIGL.GN.GCL.N.AGLA.ATMD.I...G
Retrocopy NFDSNSAYHQKEIFALQDWTQEDKRDKDAAKADLNYIGLNGNTGCLINDAGLAIATMDLIWMVG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Otolemur garnettii was not studied using RNA-Seq expression data.

ChIP-Seq

Otolemur garnettii was not studied using ChIP-Seq data.

EST

Otolemur garnettii was not studied using EST data.

TSS

Otolemur garnettii was not studied using FANTOM5 data.

Lab

retro_ogar_2196 was not experimentally validated.

Homology

Retrocopy orthology:

Otolemur garnettii does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014610	2 retrocopies	retro_acar_26, retro_acar_52,
Callithrix jacchus	ENSCJAG00000009278	2 retrocopies	retro_cjac_1233, retro_cjac_2379,
Cavia porcellus	ENSCPOG00000014961	1 retrocopy	retro_cpor_1113,
Homo sapiens	ENSG00000136143	3 retrocopies	retro_hsap_2236, retro_hsap_2281, retro_hsap_3445,
Gorilla gorilla	ENSGGOG00000008224	3 retrocopies	retro_ggor_1668, retro_ggor_1694, retro_ggor_2327,
Macaca mulatta	ENSMMUG00000007539	1 retrocopy	retro_mmul_1231,
Mustela putorius furo	ENSMPUG00000001488	1 retrocopy	retro_mputfur_768,
Nomascus leucogenys	ENSNLEG00000002948	3 retrocopies	retro_nleu_1963, retro_nleu_2140, retro_nleu_2302,
Otolemur garnettii	ENSOGAG00000006190	1 retrocopy	retro_ogar_161,
Otolemur garnettii	ENSOGAG00000007452	1 retrocopy	retro_ogar_2196 ,
Pongo abelii	ENSPPYG00000005352	2 retrocopies	retro_pabe_1939, retro_pabe_2852,
Pan troglodytes	ENSPTRG00000005859	3 retrocopies	retro_ptro_1581, retro_ptro_1615, retro_ptro_2337,