RetrogeneDB ID: retro_mmul_298

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: X:11016156..11017194(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMMUG00000009370
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ATXN3
• Ensembl ID: ENSMMUG00000020751
• Aliases: None
• Description: ataxin 3 [Source:HGNC Symbol;Acc:7106]

Sequence

>retro_mmul_298
GAAGGCTTCCTTTGTGCTCAGCACTGCCTGAATAATCTGCTGCAAGGAGAATATTTCAGTCCTGTGGAATTAGCTTCAAT
TGCACATCAGCTAGATGAAGAAGAGAGGATGAGAATGGCAGAAGGAGGAGTCACTAGTGAAGACTACCGCGCATTTTTAC
AGCAGCCTTCAGAAAACATGGATGATAGCGGCTTCTTCTCCATCCAGGTAATATGCAATGCCTTGAAGTTCTGGGGTTTA
GAGGTCATCCATTTCAATAATCCTGAATATCAGAAGCTCGGGATTGATCCTATAAATGAAAGATCTTTTATATGTAATTA
TAAACAACACTGGTTTACTATTAGAAAATTCGGAAAACACTGGTTTAACTTGAATTCTCTCTTGGCGGGTCCAGAATTAA
TATCAGATACATGCCTTGCAAATTTCTTGACTCAACTGCAACAGGAAGCATATTCTGTATTTGTTGTTAAGGGGGATCTG
CCAGACTGTGAAGCTGACCAACTGCTGCAAATCATCAGTGTTGAAGAGATGGATAGACCAAAACTTAATGGAAAAAAATT
AGCCAAAGAAAAAGACCACAGAGTCTACAAAACAATTCTTGAAAAAGTGTCAGAAGAAAGTGATGAGTCTGGAACATCAG
ACCAAGAAGAGCAGGATTTTCAGAGGGCCCTGGAACTAAGCCGCCAAGAAACCAATAAAGAAGATGAAGATCTCCGCAGG
GCTATTGAACTAAGTATGCAAGGTAGTTCCAGAAACACATCGCAAGATCTTCCAAAGACATCATGTGGAACTCCTGCTTC
GGAAGAGCCAAAGAAAATAAAAGACTATTTTGAAAAGCATCAGCAGGAACAGAAGCAGCAGCAACAACAGTCAGATCCGC
CAGGTCACAGTTCATATCTACACGAAAGGCCAACAACAAGTTCGAGAGCAATTGAGAGTGATCTCAGTGATGACGTCAAT
GAAGACATGGTACAGGCCGCTGTCGACACTGTTTTAGAAATTATGAGAAAGAATCTGAAAATCAAAGGAGAAAAATAA

Alignment

ORF - retro_mmul_298 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.62 %
• Parental protein coverage: 77.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EGSLCAQHCLNNLLQGEYFSPVELSSIAHQLDEEERMRMAEGGVTSEDYRTFLQQPSGNMDDSGFFSIQV
          EG.LCAQHCLNNLLQGEYFSPVEL.SIAHQLDEEERMRMAEGGVTSEDYR.FLQQPS.NMDDSGFFSIQV
Retrocopy EGFLCAQHCLNNLLQGEYFSPVELASIAHQLDEEERMRMAEGGVTSEDYRAFLQQPSENMDDSGFFSIQV

Parental  ISNALKVWGLELILFNSPEYQRLRIDPINERSFICNYKEHWFTVRKLGKQWFNLNSLLTGPELISDTYLA
          I.NALK.WGLE.I.FN.PEYQ.L.IDPINERSFICNYK.HWFT.RK.GK.WFNLNSLL.GPELISDT.LA
Retrocopy ICNALKFWGLEVIHFNNPEYQKLGIDPINERSFICNYKQHWFTIRKFGKHWFNLNSLLAGPELISDTCLA

Parental  LFLAQLQQEGYSIFVVKGDLPDCEADQLLQMIRVQQMHRPKLIGEELAQLKEQRVHKTDLERVLEANDGS
          .FL.QLQQE.YS.FVVKGDLPDCEADQLLQ.I.V..M.RPKL.G..LA..K..RV.KT.LE.V.E..D.S
Retrocopy NFLTQLQQEAYSVFVVKGDLPDCEADQLLQIISVEEMDRPKLNGKKLAKEKDHRVYKTILEKVSEESDES

Parental  GMLDEDEEDLQRALALSRQEIDMEDEEADLRRAIQLSMQGSSRNISQDIPQTSGTNLTSEELRKRREAYF
          G..D..E.D.QRAL.LSRQE...EDE..DLRRAI.LSMQGSSRN.SQD.P.TS.....SEE..K....YF
Retrocopy GTSDQEEQDFQRALELSRQETNKEDE--DLRRAIELSMQGSSRNTSQDLPKTSCGTPASEEPKKIKD-YF

Parental  ENN
          E..
Retrocopy EKH

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	0.00 RPM	13.45 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	8.49 RPM
SRP007412_cerebellum	0.00 RPM	15.18 RPM
SRP007412_heart	0.00 RPM	6.42 RPM
SRP007412_kidney	0.00 RPM	12.32 RPM
SRP007412_liver	0.00 RPM	3.44 RPM
SRP007412_testis	36.75 RPM	10.10 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_298 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_298 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_298 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,