RetrogeneDB ID: retro_mmul_982

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 13:32242527..32243891(+)
• Located in intron of: ENSMMUG00000030876

Retrocopy information

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

Parental gene information

• Parental gene symbol: DDX50
• Ensembl ID: ENSMMUG00000001006
• Aliases: None
• Description: ATP-dependent RNA helicase DDX50 [Source:RefSeq peptide;Acc:NP_001245111]

Sequence

>retro_mmul_982
CGATTGGATCTTTCTAAACTGTGCCACGTTGTGCTTGATAAGTGGATCAAATGTTAGATTTAGGTTTTGCTGAACAAGTT
GAAGATATTATTCATGAATCCTACAAAACTGATTCTGAAGACAATCCTCAGACTTTACTTTTTTCTGCAGCTTGCCGACA
GTGAGTATACAAAGTTGCAAAAAAATGCATGAAATCCAGATACGAACAGGTTGACCTTGTTAGAAAAATGACTCAAAAGG
CTGCAGCTACTGTGGAACATTTGGCCATCCAGTGTCATTGCTCTCAGAGGCCAGCAGTTATTGGAGATGTCCTTCCAGTC
TGCAGTGGGTCTGAAGGGAGGGCTATTATTTTCTGTGAGACCAAGAGGAATGTAACTGAAATGGCCATGAATCCACACAT
AAAACAGAATGCCCAGTGTTTACATGGGGACATTGCACAGTCACAAAGAGAAATTACACTAAAAGGATTCAGAGAAGGTA
GTTTTAAAGTTTTGGTGGCAACCAATGTGGCTGCCCGTGGTTTGGACATTCCTGAAGTTGACCTGGTGATTCAAAGTTCT
TCTCAGAATATTGAGTCCTATATCCATCATTCTGGACGCACAGGTAGAGCTGGACGGACAGGGATTTGTATTTGTTTTTA
TCAACCAAGAGAAAGAGGTCAACTAAGATATGTGGAACAAAAAGCAGGAATTACTTTTAAATGTGTAGCTGTTCCTTCTA
CAATTTATTTAGTTAAGTCTAAAAGCATGGATGCCATAAGCTCTCTGGCTTCCTTTTTTTATGCTGCTGTTGATTTTTTC
CAACCATCAGCTCAGATACTAATAGAAGAGAAAGGGGCAGTGGATGCCTTGGCTGCAGCTTTGGCCCACATTTCTGGTGC
ATCAAGCTTTGAACCACGATCTTTGATCACCTCTGATAAGGGATTTGTGACCATGAATCTGGAAAGCCTAGAGGAAATAC
AAGATGTTAGCTGTGCTTGAAAAGAACTTAACAGAAAGCTGAGTAGTAATGCAGTGTCTCAGATTACCAGAATGTGCCTC
CTGAAAGGAAATGTGGGTGTTTGCTTTGGTGTTCCTACAACTAAGTCAGAAAGGTTACAGGCAGAGTGGCATGATTCCGA
CTGGATACTCTCAGTGCCAGCCAAATTACCTGAAATTGAAGATTATTATGATGGAAACACATCCTCTAATTCCAGACAAA
GGAGTTGCTGGTCAAATGGCCAGTCGGGCTGGTCAAGTGGTTGATCTGGCAGCCGGTCAGGTAGACAGAATGGACAAAGG
AGTCGCTCAGGAAGTCGACAAGGTGGTAAAAGATGAAGTGGGAATAGAAATCGATCAAGAAGTGGGAGCTACAAACAGAG
TTTT

Alignment

ORF - retro_mmul_982 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.7 %
• Parental protein coverage: 62.28 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RLDLSKLRHVVLDE-VDQMLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSATCPQWVYKVAKKYMKSRYE
          RLDLSKL.HVVLD..VDQMLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSA.C.Q.VYKVAKK.MKSRYE
Retrocopy RLDLSKLCHVVLDK<VDQMLDLGFAEQVEDIIHESYKTDSEDNPQTLLFSAACRQ*VYKVAKKCMKSRYE

Parental  QVDLVGKMTQKAATTVEHLAIQCHWSQRPAVIGDVLQVYSGSEGRAIIFCETKKNVTEMAMNPHIKQNAQ
          QVDLV.KMTQKAA.TVEHLAIQCH.SQRPAVIGDVL.V.SGSEGRAIIFCETK.NVTEMAMNPHIKQNAQ
Retrocopy QVDLVRKMTQKAAATVEHLAIQCHCSQRPAVIGDVLPVCSGSEGRAIIFCETKRNVTEMAMNPHIKQNAQ

Parental  CLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSPPQDVESYIHRSGRTGRAGRTG
          CLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSS..Q..ESYIH.SGRTGRAGRTG
Retrocopy CLHGDIAQSQREITLKGFREGSFKVLVATNVAARGLDIPEVDLVIQSSS-QNIESYIHHSGRTGRAGRTG

Parental  ICICFYQPRERGQLRYVEQKAGITFKRVGVPSTMDLVKSKSMDAIRSLASVSYAAVDFFRPSAQRLIEEK
          ICICFYQPRERGQLRYVEQKAGITFK.V.VPST..LVKSKSMDAI.SLAS..YAAVDFF.PSAQ.LIEEK
Retrocopy ICICFYQPRERGQLRYVEQKAGITFKCVAVPSTIYLVKSKSMDAISSLASFFYAAVDFFQPSAQILIEEK

Parental  GAVDALAAALAHISGASSFEPRSLITSDKGFVTMTLESLEEIQDVSCAWKELNRKLSSNAVSQITRMCLL
          GAVDALAAALAHISGASSFEPRSLITSDKGFVTM.LESLEEIQDVSCA.KELNRKLSSNAVSQITRMCLL
Retrocopy GAVDALAAALAHISGASSFEPRSLITSDKGFVTMNLESLEEIQDVSCA*KELNRKLSSNAVSQITRMCLL

Parental  KGNMGVCFDVPTTESERLQAEWHDSDWILSVPAKLPEIEEYYDGNTSSNSRQRSGWSSGRSGRSGRSGGR
          KGN.GVCF.VPTT.SERLQAEWHDSDWILSVPAKLPEIE.YYDGNTSSNSRQRS.WS.G.SG.S....G.
Retrocopy KGNVGVCFGVPTTKSERLQAEWHDSDWILSVPAKLPEIEDYYDGNTSSNSRQRSCWSNGQSGWS---SG*

Parental  SGGRSGRQSRQGSRSGSRQDGRRRSGNRNRSRSGGHKRSF
          SG.RSGRQ..Q.SRSGSRQ.G.R.SGNRNRSRSG..K.SF
Retrocopy SGSRSGRQNGQRSRSGSRQGGKR*SGNRNRSRSGSYKQSF

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	0.34 RPM	26.22 RPM
SRP007412_brain_prefrontal_cortex	0.24 RPM	17.06 RPM
SRP007412_cerebellum	0.32 RPM	39.33 RPM
SRP007412_heart	0.18 RPM	19.84 RPM
SRP007412_kidney	0.23 RPM	26.53 RPM
SRP007412_liver	0.08 RPM	12.27 RPM
SRP007412_testis	0.04 RPM	42.41 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_982 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_982 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_982 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2089
Pan troglodytes	retro_ptro_1536
Pongo abelii	retro_pabe_2007

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018844	1 retrocopy	retro_cjac_1298,
Homo sapiens	ENSG00000107625	2 retrocopies	retro_hsap_2089, retro_hsap_2866,
Macaca mulatta	ENSMMUG00000001006	1 retrocopy	retro_mmul_982 ,
Mus musculus	ENSMUSG00000020076	1 retrocopy	retro_mmus_3362,
Nomascus leucogenys	ENSNLEG00000011631	2 retrocopies	retro_nleu_1300, retro_nleu_609,
Otolemur garnettii	ENSOGAG00000001844	2 retrocopies	retro_ogar_1492, retro_ogar_555,
Pongo abelii	ENSPPYG00000002390	3 retrocopies	retro_pabe_2007, retro_pabe_2369, retro_pabe_2418,
Pan troglodytes	ENSPTRG00000002562	2 retrocopies	retro_ptro_1536, retro_ptro_1938,