RetrogeneDB ID: retro_nleu_66

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397281.1:10640110..10641175(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000018731
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSNLEG00000017126
• Aliases: None
• Description: None

Sequence

>retro_nleu_66
ATGGATTTCATCTTTCATGAGAAACAAGAAGGTTTCCTGTGTGCTCAGCACTGTTTGAACAATCTACTGCAAGGAGAATA
TTTTAGCCCTGTGGAATTAGCCTCAATTGCACATCAGCTAGATGAAGAAGAGAGGATGAGAATGGCAGAAGGGGGAGTCA
CCAGTGAAGAGTATCTCGCATTTTTACAGCAGCCTTCAGAAAACATGGATGATACCGGTTTCTTCTCCATTCAGGTAATA
AGCAATGCCTTGAAGTTCTGGGGTTTAGACATCATCCATTTCAATAATCCTGAATATCAGAAGCTCGGGATTGATCCTAT
AAATGAAAGATCTTTTATATGTAATTATAAACAACACTGGTTTACCATTAGAAAATTCGGAAAACACTGGTTTAACTTGA
ATTCTCTCTTGGCGGGTCCAGAATTAATATCAGATACATGCCTTGCAAATTTCTTGGCTCGATTACAACAACAAGCATAT
TCTGTATTTGTTATCAAGGGTGATCTGCCAGACTGTGAAGCTGACCAACTCCTGCAGATCATCAGTGTCGAAGAGATGGA
TACACCAAAACTTAATGGAAAAAAATTACTAAAAGAAAAAGAGCATAGAGTCTATAAAACATTCCTTGAAAAAGTGTTAG
AAGAAAGTGATGAGTCTGAAACATCAGACCAAGATGAGGATTTTCAGAGGGCCCTTGAACTAAGTCGCCAAGAGGCCAAT
AGAGAAGATGAAGATCTCCGCAGGGCTACTGAGCTAAGCATGCCAGGTAGTTCCAGAAACACATCACAAGACCTTCCAAA
GACATCATGTGTAACTCCTGCTTCGGAACAGCCGAAGAAAATAAAAGAAGACTATTTTGAAAAGCATCAGCAGGAACAGA
AGCAGCAGCAACAACAGTCAGATCCGCCAGGTCGCAGTTCATATCTACACGAAAGGCCAACAACAAGTTCGAGAGCAATT
GAGAGTGATCTCAGTGATGACATCAATGAAGACACGGTACAGGCCACTGTCGACACCGTTTTAGAAATTATGAGAAAGAA
GTTGAAAATCAAAGGAGAAAAATAA

Alignment

ORF - retro_nleu_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.18 %
• Parental protein coverage: 98.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MESIFHEKQEGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMD
          M..IFHEKQEG.LCAQHCLNNLLQGEYFSPVEL.SIAHQLDEEERMRMAEGGVTSE.Y..FLQQPS.NMD
Retrocopy MDFIFHEKQEGFLCAQHCLNNLLQGEYFSPVELASIAHQLDEEERMRMAEGGVTSEEYLAFLQQPSENMD

Parental  DSGFFSIQVISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWLNLGSLQAPP
          D.GFFSIQVISNALK.WGL..I.FN.PEYQ.L.IDPINERSFICNYK.HWFT.RK.GK.W.NL.SL.A.P
Retrocopy DTGFFSIQVISNALKFWGLDIIHFNNPEYQKLGIDPINERSFICNYKQHWFTIRKFGKHWFNLNSLLAGP

Parental  PGFTPFSCLSLSEQMQLGSYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVHKTDLE
          ...............Q...YS.FV.KGDLPDCEADQLLQ.I.V..M..PKL.G..L...KE.RV.KT.LE
Retrocopy ELISDTCLANFLARLQQQAYSVFVIKGDLPDCEADQLLQIISVEEMDTPKLNGKKLLKEKEHRVYKTFLE

Parental  RVLETNDGSGMLDEDEEDLQRALALSRQEIDMEDEEADLRRAIQLSMQGSSRNISQDIPQTSGTNLTSEE
          .VLE..D.S...D.D.ED.QRAL.LSRQE...EDE..DLRRA..LSM.GSSRN.SQD.P.TS.....SE.
Retrocopy KVLEESDESETSDQD-EDFQRALELSRQEANREDE--DLRRATELSMPGSSRNTSQDLPKTSCVTPASEQ

Parental  LRKRREAYFEKQQQQQQQQQQQQQEDLSGQSSHPCERPTTSSGALGSDLGDAMSEEDMLQAAVTMSLETV
          ..K..E.YFEK...QQ.Q.QQQQQ.D..G.SS...ERPTTSS.A..SDL.D....ED..QA.V...LE..
Retrocopy PKKIKEDYFEK--HQQEQKQQQQQSDPPGRSSYLHERPTTSSRAIESDLSDDIN-EDTVQATVDTVLEIM

Parental  RNDLKTEGK
          R..LK..G.
Retrocopy RKKLKIKGE

Legend:

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

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_66 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys 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 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,