RetrogeneDB ID: retro_pabe_9

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: X:13229999..13231067(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000020129
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSPPYG00000006075
• Aliases: None
• Description: ataxin 3 [Source:HGNC Symbol;Acc:7106]

Sequence

>retro_pabe_9
ATGGATTTCATCTTTCATGAGAAACAGGAAGGTTTCTTGTGTGCTCAGCACTGTCTGAACAATCTATTGCAAGGAGAATA
TTTTAGCCCTGTGGAATTAGCCTCAATTGCACATCAGCTAGATGAAGAAGAGAGGATGAGAATGGCAGAAGGAGGAGTCA
CCAGTGAAGAGTATCTCGCATTTTTACAGCAGCCTTCAGAAAACATGGATGATACCGGTTTCTTCTCCATTCAGGTAATA
AGCAATGCCTTGAAGTTCTGGGGTTTAGAGATCATCCATTTCAATAATCCTGAATATCAGAAGCTCGGCATTGATCCTAT
AAATGAAAGATCTTTTATATGTAATTATAAACAACACTGGTTTACTATTAGAAAATTCGGAAAACACTGGTTTAACTTGA
ATTCTCTCTTGGCAGGGCCAGAATTAGTATCAGATACATGCCTTGCAAATTTCTTGGCTCGATTACAACAACAAGCATAT
TCTGTATTTGTTGTCAAGGGTGATCTGCCAGACTGTGAAGCTGACCAACTCCTGCAGATCATCAGTGTCGAAGAGATGGA
TACACCAAAACTTAATGGAAAAAAATCAGTAAAAGAAAAAGAGCACAGAGTCTATAAAACAGTCCTTGAAAAAGTGTCAG
AAGAAAGTGATGAGTCTGGAACATCAGACCAAGATGACGAGGATTTTCAGAGGACCCTTGAACTAAGCCGCCAAGAAACC
AATAGAGAAGATGAAGACCTCCGCAGGGCTATTGAGCTAAGCATGCAAGGTAGTTCTGGAAACACATCGCAAGATCTTCC
AAAGACATCATGTGTAACTCCTGCTTCAGAACAGCCGAAGAAAATAAAAGAGGACTATTTTGAACAGCATCAGCAGGAAC
AGAAGCTGCAGCAACAACAGTCAGATCTGCCAGGTTACAGTTCATATATACACGAAAGGCCAACAACAAGTTCGAGAGCA
ATTGAGAGTGACCTCAGTGATGACATCAGTGAAGACACAGTACAGGCCGCTGTCGACACCGTTTTAGAAATTATGAGAAA
GAATTTGAAAATCAAAGGAGAAAAATAA

Alignment

ORF - retro_pabe_9 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.87 %
• Parental protein coverage: 96.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLEEEERMRMAEGGVSSEVFRTFLQQPSGNMDDSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPIN
          QL.EEERMRMAEGGV.SE....FLQQPS.NMDD.GFFSIQVISNALK.WGLE.I.FN.PEYQ.L.IDPIN
Retrocopy QLDEEERMRMAEGGVTSEEYLAFLQQPSENMDDTGFFSIQVISNALKFWGLEIIHFNNPEYQKLGIDPIN

Parental  ERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTYLALFLAQLQQEGYSIFVVKGDLPDCEADQLL
          ERSFICNYK.HWFT.RK.GK.WFNLNSLL.GPEL.SDT.LA.FLA.LQQ..YS.FVVKGDLPDCEADQLL
Retrocopy ERSFICNYKQHWFTIRKFGKHWFNLNSLLAGPELVSDTCLANFLARLQQQAYSVFVVKGDLPDCEADQLL

Parental  QMIRVQQMHRPKLIGEELAQLKEQRVHKTDLERVLEANDGSGMLDEDEEDLQRALALSRQEIDMEDEEAD
          Q.I.V..M..PKL.G......KE.RV.KT.LE.V.E..D.SG..D.D.ED.QR.L.LSRQE...EDE..D
Retrocopy QIISVEEMDTPKLNGKKSVKEKEHRVYKTVLEKVSEESDESGTSDQDDEDFQRTLELSRQETNREDE--D

Parental  LRRAIQLSMQGSSRNISQDIPQTSGTNLTSEELRKRREAYFEKQQQKQQQQQQQQQQGDLSGQSSHPCER
          LRRAI.LSMQGSS.N.SQD.P.TS.....SE...K..E.YFE...Q.QQ.Q..QQQQ.DL.G.SS...ER
Retrocopy LRRAIELSMQGSSGNTSQDLPKTSCVTPASEQPKKIKEDYFE---QHQQEQKLQQQQSDLPGYSSYIHER

Parental  PTTSSGALGSDLGDAMSEEDMLQAAVTMSLETVRNDLKTEGKK
          PTTSS.A..SDL.D..S.ED..QAAV...LE..R..LK..G.K
Retrocopy PTTSSRAIESDLSDDIS-EDTVQAAVDTVLEIMRKNLKIKGEK

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain_prefrontal_cortex	0.06 RPM	9.18 RPM
SRP007412_cerebellum	0.00 RPM	6.44 RPM
SRP007412_heart	0.03 RPM	3.46 RPM
SRP007412_kidney	0.03 RPM	5.24 RPM
SRP007412_liver	0.09 RPM	4.62 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_9 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_9 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_9 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005786	2 retrocopies	retro_btau_1652, retro_btau_330,
Choloepus hoffmanni	ENSCHOG00000005302	1 retrocopy	retro_chof_2238,
Callithrix jacchus	ENSCJAG00000018025	2 retrocopies	retro_cjac_1724, retro_cjac_375,
Cavia porcellus	ENSCPOG00000010887	1 retrocopy	retro_cpor_1460,
Homo sapiens	ENSG00000066427	1 retrocopy	retro_hsap_89,
Macaca mulatta	ENSMMUG00000020751	1 retrocopy	retro_mmul_298,
Monodelphis domestica	ENSMODG00000002006	2 retrocopies	retro_mdom_1498, retro_mdom_1573,
Nomascus leucogenys	ENSNLEG00000017126	1 retrocopy	retro_nleu_66,
Pongo abelii	ENSPPYG00000006075	1 retrocopy	retro_pabe_9 ,
Tupaia belangeri	ENSTBEG00000008099	3 retrocopies	retro_tbel_102, retro_tbel_2635, retro_tbel_3925,