RetrogeneDB ID: retro_mmul_827

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:90904093..90905009(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL2
• Ensembl ID: ENSMMUG00000002450
• Aliases: None
• Description: None

Sequence

>retro_mmul_827
ATGATCCTGTGGGCACTGACCTGTACTCTGCATTCTCTGAGCCTGGCACCCCCGACCATTGCCACTCCTGTCCCAAGTCT
GTTCCCTGCCTCCCAGGTGATGAACAATGCCCTCTTCCAATGGCCCTCTGCCTTGATGTTGCTCCCCTGCCACCAAATCC
TTACTTCTATGGCCCTTAGTGCCAACTTTGTGTCTTGAAAGAGTCATACCAAGTACACCATTAAACCAGTGAAGATGAAG
AAGTCTGGGGGTGAAGATCACACAGGCCAGATCCGGGTGCATGGTATTGGCAGGGGCCACAAGCAACATTATTGCATGAT
TGACTTTTGTGTTTCTGGCCTGAGGAAGAGACCAAATCAGGACCCTTTGAGGAGAAGGTTATCCAAGTCCACTGTGATCC
CTGTAGGTCAACAGACATAGCTCTGGCTGCTGGGGCAGCCAGAAACACTGGATCATCGCCATAGAAAACAAGCAGGCTGG
AGATACCATCCTGAACTCTAACCACATAGGCCGAATGGCAGTTGCTGCTCAGGAAGGGGATGCGCATCCACTTGGGACTC
TGCCTTTGGCGACCCTCATCAACAGCATGGAAAGTGAGCGAGGCCAGGGTGCCCAGTATATCCGAGCTGCAGGGACGTGC
GGTGTGCTACTGTGGAAGGTGAATGGCACAGCCATTATCCAGCTGCCCTTTAAGAGGCAGATGCAGGTGCTGGAAACATG
CATAGCAACAGTAGGCTAAGTATCCAACACTGATCATAACAAACAGGTCACTGGCAGGGCAGGTCACAACCACTGACTGG
GCAAGAAGCCTTCCAGTGGGCTATGGCACCGCAAGGGGTGCTGGGCTGGCCGAAAGAGTTGGCCACTACCATTCATGAAG
AGTTATGTGAAACTGCCTTCTGCTGCTGCCCAAAGC

Alignment

ORF - retro_mmul_827 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.87 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MALWALTRALRSLSLAPPTVATPAPSLFPAAQMMNNALLQQPSALMLLPCRPILTSLALNANFVSWKSRT
          M.LWALT..L.SLSLAPPT.ATP.PSLFPA.Q.MNNAL.Q.PSALMLLPC..ILTS.AL.ANFVS.KS.T
Retrocopy MILWALTCTLHSLSLAPPTIATPVPSLFPASQVMNNALFQWPSALMLLPCHQILTSMALSANFVS*KSHT

Parental  KYTIAPVKMRKSGGRDHTGRIRVHGIGGGHKQRYRMIDF-LRFRPEE-TKSGPFEEKVIQVRYDPCRSAD
          KYTI.PVKM.KSGG.DHTG.IRVHGIG.GHKQ.Y.MIDF.L.F.PEE.TKSGPFEEKVIQV..DPCRS.D
Retrocopy KYTIKPVKMKKSGGEDHTGQIRVHGIGRGHKQHYCMIDF<LCFWPEEETKSGPFEEKVIQVHCDPCRSTD

Parental  IALVAG-GSRKRWIIATENMQAGDTVLNSNHIGRMAVAAREGDAHPLGALPVGTLINNVESEPGRGAQYI
          IAL.AG.GS.K.WIIA.EN.QAGDT.LNSNHIGRMAVAA.EGDAHPLG.LP..TLIN..ESE.G.GAQYI
Retrocopy IALAAG<GSQKHWIIAIENKQAGDTILNSNHIGRMAVAAQEGDAHPLGTLPLATLINSMESERGQGAQYI

Parental  RAAGTCGVLLRKVNGTAIIQLPSKRQMQVLETCIATVGRVSNVDHNKRVIGKAGRNRWLGKRPNSGRWHR
          RAAGTCGVLL.KVNGTAIIQLP.KRQMQVLETCIATVG.VSN.DHNK.V.G.AG.N..LGK.P.SG.WHR
Retrocopy RAAGTCGVLLWKVNGTAIIQLPFKRQMQVLETCIATVG*VSNTDHNKQVTGRAGHNH*LGKKPSSGLWHR

Parental  KGGWAGRKIRPLPPMKSYVKLPSAAAQS
          KG.WAGRK..PLP.MKSYVKLPSAAAQS
Retrocopy KGCWAGRKSWPLPFMKSYVKLPSAAAQS

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	14.23 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	26.02 RPM
SRP007412_cerebellum	0.00 RPM	14.21 RPM
SRP007412_heart	0.00 RPM	20.49 RPM
SRP007412_kidney	0.12 RPM	20.30 RPM
SRP007412_liver	0.04 RPM	56.41 RPM
SRP007412_testis	0.00 RPM	34.94 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_827 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_827 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_827 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_1039
Pan troglodytes	retro_ptro_709
Gorilla gorilla	retro_ggor_820
Pongo abelii	retro_pabe_871

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000005134	1 retrocopy	retro_acar_136,
Callithrix jacchus	ENSCJAG00000005116	1 retrocopy	retro_cjac_3318,
Homo sapiens	ENSG00000112651	1 retrocopy	retro_hsap_1039,
Gorilla gorilla	ENSGGOG00000010552	1 retrocopy	retro_ggor_820,
Macaca mulatta	ENSMMUG00000002450	1 retrocopy	retro_mmul_827 ,
Nomascus leucogenys	ENSNLEG00000004370	1 retrocopy	retro_nleu_912,
Otolemur garnettii	ENSOGAG00000034421	2 retrocopies	retro_ogar_1582, retro_ogar_1842,
Pongo abelii	ENSPPYG00000016630	1 retrocopy	retro_pabe_871,
Pan troglodytes	ENSPTRG00000018186	1 retrocopy	retro_ptro_709,
Rattus norvegicus	ENSRNOG00000018057	1 retrocopy	retro_rnor_555,