RetrogeneDB ID: retro_mmul_637

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 10:54144686..54145198(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS11
• Ensembl ID: ENSMMUG00000013659
• Aliases: None
• Description: 28S ribosomal protein S11, mitochondrial [Source:RefSeq peptide;Acc:NP_001248507]

Sequence

>retro_mmul_637
ATCATGGCCAGGATGCTGGTGCAGACCATCCACACAGGCACCCAGAAGCTCCAAGACATTGAGGCCAAGCAGAATGTTGA
AGAGAAGATGGTCGTTCCCAACCACACCGGCTTTAGCATTTACCCTTCCAATCCAAAAGAAAAAAGCTCTCTGAGGTGGG
CAGGAAAATTTGAGGAGGTCCAAATTGCACACATTAAAGCATCCTACAACAACACAGAGATCCAGGTAATCTCGGCCACT
AATCAGCCCTTTGCCCATACTTTCTGTGGCACAGAGGAATTTCTGAATGCCGAGAAGGAGGCAGGCATTGATGCACAGAC
AGCAGGCATAGCAGCAGCGACAAAAGCTACAGGAAAGGGTGTTACCCACATCTGAGTTGTGGTGAAAGGCCAGGGGCCAG
GACACCTGTCTGCCATCGAGGGACTGATCATGGGTGGCCTGGAAGTGATCTCAATCACCACAACACCCCCATCCCACACA
ATGGCTTCTGCCCCAGGAAGGCTCCAAGGCTG

Alignment

ORF - retro_mmul_637 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.94 %
• Parental protein coverage: 88.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVARTPARTIHTDARQLQDAAAKQEVEEKAAAPSHTRFSIYPPIPGEESSLRWAGKKFEEIPIAHIKASY
          ..AR....TIHT....LQD..AKQ.VEEK...P.HT.FSIYP..P.E.SSLRWAGK.FEE..IAHIKASY
Retrocopy IMARMLVQTIHTGTQKLQDIEAKQNVEEKMVVPNHTGFSIYPSNPKEKSSLRWAGK-FEEVQIAHIKASY

Parental  NNTQIQVVSASNEPLARASCGTEGFRNSKKGTGIAAQTAGIAAAAKATQKGVTHIRVVVKGLGPGRLSAI
          NNT.IQV.SA.N.P.A...CGTE.F.N..K..GI.AQTAGIAAA.KAT.KGVTHI.VVVKG.GPG.LSAI
Retrocopy NNTEIQVISATNQPFAHTFCGTEEFLNAEKEAGIDAQTAGIAAATKATGKGVTHI*VVVKGQGPGHLSAI

Parental  HGLTMGGLEVISIT-DNTPIPHNGCRPRKARRL
          .GL.MGGLEVISIT..NTPIPHNG..PRKA.RL
Retrocopy EGLIMGGLEVISIT<HNTPIPHNGFCPRKAPRL

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	10.31 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	18.17 RPM
SRP007412_cerebellum	0.06 RPM	10.53 RPM
SRP007412_heart	0.00 RPM	14.13 RPM
SRP007412_kidney	0.00 RPM	12.79 RPM
SRP007412_liver	0.00 RPM	15.56 RPM
SRP007412_testis	0.00 RPM	13.31 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_637 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_637 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_637 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2458
Gorilla gorilla	retro_ggor_1531
Pan troglodytes	retro_ptro_1419

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000013012	2 retrocopies	retro_cjac_2601, retro_cjac_2989,
Felis catus	ENSFCAG00000014967	1 retrocopy	retro_fcat_282,
Homo sapiens	ENSG00000181991	1 retrocopy	retro_hsap_2458,
Gorilla gorilla	ENSGGOG00000015152	1 retrocopy	retro_ggor_1531,
Macaca mulatta	ENSMMUG00000013659	1 retrocopy	retro_mmul_637 ,
Nomascus leucogenys	ENSNLEG00000011441	1 retrocopy	retro_nleu_1902,
Ochotona princeps	ENSOPRG00000008247	1 retrocopy	retro_opri_540,
Pongo abelii	ENSPPYG00000006751	2 retrocopies	retro_pabe_1808, retro_pabe_2583,
Pan troglodytes	ENSPTRG00000007420	1 retrocopy	retro_ptro_1419,