RetrogeneDB ID: retro_mmul_1684

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 3:69983880..69984408(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1951
• Ensembl ID: ENSMMUG00000005673
• Aliases: None
• Description: ribonuclease T2 precursor [Source:RefSeq peptide;Acc:NP_001253654]

Sequence

>retro_mmul_1684
CTGTGCCAGGCCTGGCCTGAGACAGTATGTGAGAAAGTGCAGAACGACTGTGGGGCCCCTCCGGATTACTGAACAATACG
TGGACTATGGCCCGATAAAAATGAAGGATGTAATGGATCGTGGCACTTTAATTTAGAAGAGATTAAGGATATTTTGCCGG
AAATGAAGGCACACTGGCCTGATGTAATTCACTCGTTTCCCAATCGTAGCCACTTCTAGAAGCATGAGAGGGAAAAGCAT
GGAACCTGTGCCGCAGTGGTGGACGCACTCAACTCCCAAAAGTACTTCAGCAGAAGCCTGGAACTCTACAGGGAGCTGGA
CCCCAACAGTGTGCTCCTAAAACTGCGTCTAAGCGCATCCATCAATTACTAACAAGTTGCAGATTTTAAAGATGCCCTTG
TCAGAGTGTATGAAGTGATACCCAAAATCCAGTGCCTTCCGCGAAGCCAGGATGGGAAAGTATAGACAATTGGTCAGATA
GAACCTTGCCTCGCTGAGCAAGACCAGTAGCTGCAAAACTGCATGGAG

Alignment

ORF - retro_mmul_1684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.1 %
• Parental protein coverage: 69.14 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MVQHWPETVCEKIQNDCRDPPDYWTIHGLWPDKSEGCNRSWPFNLEEIKDLLPEMKAYWPDVIHSFPNRS
          ..Q.WPETVCEK.QNDC..PPDY.TI.GLWPDK.EGCN.SW.FNLEEIKD.LPEMKA.WPDVIHSFPNRS
Retrocopy LCQAWPETVCEKVQNDCGAPPDY*TIRGLWPDKNEGCNGSWHFNLEEIKDILPEMKAHWPDVIHSFPNRS

Parental  RFWKHEWEKHGTCAAQVDALNSQKKYFGRSLELYRELDLNSVLLKLGIKPSINYYQVADFKDALARVYGV
          .F.KHE.EKHGTCAA.VDALNSQ.KYF.RSLELYRELD.NSVLLKL....SINY.QVADFKDAL.RVY.V
Retrocopy HF*KHEREKHGTCAAVVDALNSQ-KYFSRSLELYRELDPNSVLLKLRLSASINY*QVADFKDALVRVYEV

Parental  IPKIQCLPPSQDEEVQTVGQIELCLTKQDQQLQNCTE
          IPKIQCLP.SQD..V.T.GQIE.CL..QDQ.LQNC.E
Retrocopy IPKIQCLPRSQDGKV*TIGQIEPCLAEQDQ*LQNCME

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	0.78 RPM	14.12 RPM
SRP007412_brain_prefrontal_cortex	1.35 RPM	16.82 RPM
SRP007412_cerebellum	0.13 RPM	5.23 RPM
SRP007412_heart	0.41 RPM	21.96 RPM
SRP007412_kidney	0.23 RPM	37.68 RPM
SRP007412_liver	0.08 RPM	31.27 RPM
SRP007412_testis	0.11 RPM	7.31 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1684 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1684 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1684 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003359	1 retrocopy	retro_lafr_764,
Microcebus murinus	ENSMICG00000014184	1 retrocopy	retro_mmur_1544,
Macaca mulatta	ENSMMUG00000005673	1 retrocopy	retro_mmul_1684 ,
Monodelphis domestica	ENSMODG00000006193	1 retrocopy	retro_mdom_1994,
Nomascus leucogenys	ENSNLEG00000011573	1 retrocopy	retro_nleu_3005,
Pongo abelii	ENSPPYG00000017277	1 retrocopy	retro_pabe_3128,
Pan troglodytes	ENSPTRG00000018796	1 retrocopy	retro_ptro_2529,