RetrogeneDB ID: retro_mmul_577

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:204003040..204003804(-)
• Located in intron of: ENSMMUG00000001565

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.2811
• Ensembl ID: ENSMMUG00000006626
• Aliases: None
• Description: UAP56-interacting factor [Source:RefSeq peptide;Acc:NP_001253404]

Sequence

>retro_mmul_577
CAGCAATTTAGGATGAGAATACAATGGGTACTCCAACAGAATTCTGGTGTTGGTAAAACCAGTCTAAGCTGTAGAGGAAG
AGTAATGCCTAGAAAGAGACATCCTCATGGATAATCATTGGCCTTGCAGTTAGGAAATCATCTGGAATTGGAAAAGGAAT
TAGTCCTATGAATTGTCCATGTCTAACTGACAAGAATACAAAACACTACTTTCCAGTGTTAAAAAGAAAGGCAAGCCTTC
TGAAACAAAATGAAGTATGTAGGAAACCAGTTGCAGGTCTCAAGAGACCTAACCAGCTAAACAGAAAAAATAACATTACA
GCCAATTTTACCAGGAGAAGAAATAAATTAAGCCATCAGAAAGACACTTCACAGGTAACTTTTCTTTTCGGAAGAGGCCT
GAAGAAGGTTCAGGCCCAGTTGAACACGGAGCAACTGCTAGATGATGTAGTAGCAAAGAGAACTAGTCAACGCCAGACTT
CTATCAGAAACGCAGGAATCTGACTGTATCTACTGACAACCCTGGAGCAGTACAATGCCCAGCAACTGAGAAACCATGAT
TAATTCACACTGCTGTACCTTCATTCTTTAAAAAACAGCAGCAAAAGAATATAAAGAAAAGTTCCCGTGGGTGTTTCCCT
ACAATCTGACATAAATAGTGTTGGAAAACAGACAGAGATAGTTTTGAATGAGCAGTTTGGGATCCTGAGAAAACAAAGAG
CCACTCTCACATGTAACAAAGGGGGAAGTCACTTTTTAACTGTG

Alignment

ORF - retro_mmul_577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.48 %
• Parental protein coverage: 79.87 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RQFRMRVRWGIQQNSGFGKTSLNRRGRVMPGKRRPNG-VITGLAARKTTGIRKGISPMNRPPLSDKNIEQ
          .QFRMR..W..QQNSG.GKTSL..RGRVMP.KR.P.G..I.GLA.RK..GI.KGISPMN.P.L.DKN...
Retrocopy QQFRMRIQWVLQQNSGVGKTSLSCRGRVMPRKRHPHG<IIIGLAVRKSSGIGKGISPMNCPCLTDKNTKH

Parental  YFPVLKRKANLLRQNEGQRKPVAVLKRPNQLNRKNNIPANFTRSGNKLNHQKDTRQATFLFRRGL-KVQA
          YFPVLKRKA.LL.QNE..RKPVA.LKRPNQLNRKNNI.ANFTR..NKL.HQKDT.Q.TFLF.RGL.KVQA
Retrocopy YFPVLKRKASLLKQNEVCRKPVAGLKRPNQLNRKNNITANFTRRRNKLSHQKDTSQVTFLFGRGLKKVQA

Parental  QLNTEQLLDDVVAKRTRQWRTSTTNGGI-LTVSIDNPGAVQCPVTQKPRLTRTAAPSFLTKREQSDA-RK
          QLNTEQLLDDVVAKRT.Q..TS..N.GI.LTVS.DNPGAVQCP.T.KP.L..TA.PSF..K..Q....RK
Retrocopy QLNTEQLLDDVVAKRTSQRQTSIRNAGI<LTVSTDNPGAVQCPATEKP*LIHTAVPSFFKKQQQKNI>RK

Parental  VPKGVPLQFDINSVGKQTGMTLNERFGILKEQRATLTYNKGGSRFVTV
          VP.GV.LQ.DINSVGKQT...LNE.FGIL..QRATLT.NKGGS.F.TV
Retrocopy VPVGVSLQSDINSVGKQTEIVLNEQFGILRKQRATLTCNKGGSHFLTV

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	60.62 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	40.78 RPM
SRP007412_cerebellum	0.13 RPM	68.06 RPM
SRP007412_heart	0.00 RPM	42.81 RPM
SRP007412_kidney	0.00 RPM	33.68 RPM
SRP007412_liver	0.00 RPM	14.41 RPM
SRP007412_testis	0.00 RPM	72.97 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_577 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_577 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_577 has 5 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_476
Pan troglodytes	retro_ptro_357
Gorilla gorilla	retro_ggor_450
Pongo abelii	retro_pabe_258
Callithrix jacchus	retro_cjac_1639

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014874	1 retrocopy	retro_btau_1572,
Canis familiaris	ENSCAFG00000029695	1 retrocopy	retro_cfam_70,
Choloepus hoffmanni	ENSCHOG00000002881	2 retrocopies	retro_chof_1068, retro_chof_114,
Callithrix jacchus	ENSCJAG00000016488	2 retrocopies	retro_cjac_1639, retro_cjac_623,
Cavia porcellus	ENSCPOG00000011463	2 retrocopies	retro_cpor_1039, retro_cpor_586,
Dasypus novemcinctus	ENSDNOG00000007807	6 retrocopies	retro_dnov_1010, retro_dnov_1224, retro_dnov_1311, retro_dnov_2013, retro_dnov_442, retro_dnov_570,
Erinaceus europaeus	ENSEEUG00000001433	1 retrocopy	retro_eeur_13,
Echinops telfairi	ENSETEG00000000700	1 retrocopy	retro_etel_765,
Homo sapiens	ENSG00000122068	2 retrocopies	retro_hsap_4291, retro_hsap_476,
Gorilla gorilla	ENSGGOG00000011665	1 retrocopy	retro_ggor_450,
Macaca mulatta	ENSMMUG00000006626	1 retrocopy	retro_mmul_577 ,
Nomascus leucogenys	ENSNLEG00000015547	2 retrocopies	retro_nleu_1047, retro_nleu_889,
Pongo abelii	ENSPPYG00000014456	2 retrocopies	retro_pabe_258, retro_pabe_3497,
Pan troglodytes	ENSPTRG00000015796	1 retrocopy	retro_ptro_357,
Sorex araneus	ENSSARG00000009996	1 retrocopy	retro_sara_148,
Sarcophilus harrisii	ENSSHAG00000005704	1 retrocopy	retro_shar_242,
Tupaia belangeri	ENSTBEG00000005595	4 retrocopies	retro_tbel_2469, retro_tbel_2943, retro_tbel_4257, retro_tbel_791,