RetrogeneDB ID: retro_mmul_412

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 1:128970837..128971414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MMU.1747
• Ensembl ID: ENSMMUG00000015010
• Aliases: None
• Description: None

Sequence

>retro_mmul_412
AATGAGCTCATCCTGGGCTGGTAGGCTACAGGCCATGACATCACAGAGCACTCTGTGGTGATTCATAAGTACTATAGCCT
GATGGCCTCCAACCCCATCCACCTCACTGTGGTCACAAGTCTCCAGAACCGCTGCGTGAGCATCAAACCCTATGTCAGCA
CTTTAATGGGTGTCCTTGGGAGGACCATGGGAGTGATGTTCACACCTCTGACAGTGATATATGCATACTATTGACACTGA
ACACATTGAAGTTGACCTGATTATGAAGACCTGTTTTAACCCCAACTAAGGTATCGGACTCTCAAGTGAGTTGCAGCAAG
TAGGAGGGGCATCAGCTTGCATCCAGGATGCCCTAAGCACAGTGTTGCAATATGTAGAGGATGTACTGTCTGGAAAGATG
TCAGCTGACAATACTGTGGGCCACTTCTTAACGAGCCTTGTTAAGCAAGTACCCAAAATAGTTCCCAATGATTTCGAGAC
CATGCTCATCAGCAACATCAATGACCTGCTGATGGTGACCTACCTGGTCAATGTCACACAGTCACAGACTGCCCTCAATG
AGAAACTTGTAAACCTG

Alignment

ORF - retro_mmul_412 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 53.19 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NELILGWYATGHDITEHSVLIHEYYSREAPNPIHLTVDTSLQNGRMSIKAYVSTLMGVPGRTMGVMFTPL
          NELILGW.ATGHDITEHSV.IH.YYS..A.NPIHLTV.TSLQN...SIK.YVSTLMGV.GRTMGVMFTPL
Retrocopy NELILGW*ATGHDITEHSVVIHKYYSLMASNPIHLTVVTSLQNRCVSIKPYVSTLMGVLGRTMGVMFTPL

Parental  TVKYAYY-DTERIGVDLIMKTCFSPNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSADNTV
          TV.YAYY.DTE.I.VDLIMKTCF.PN..IGLSS.LQQVGGASA.IQDALSTVLQY.EDVLSGK.SADNTV
Retrocopy TVIYAYY>DTEHIEVDLIMKTCFNPN*GIGLSSELQQVGGASACIQDALSTVLQYVEDVLSGKMSADNTV

Parental  GRFLMSLVNQVPKIVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL
          G.FL.SLV.QVPKIVP.DFETML.SNINDLLMVTYL.N.TQSQ.ALNEKLVNL
Retrocopy GHFLTSLVKQVPKIVPNDFETMLISNINDLLMVTYLVNVTQSQTALNEKLVNL

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	0.90 RPM	44.93 RPM
SRP007412_brain_prefrontal_cortex	0.32 RPM	56.72 RPM
SRP007412_cerebellum	0.58 RPM	49.53 RPM
SRP007412_heart	0.29 RPM	68.19 RPM
SRP007412_kidney	0.35 RPM	80.05 RPM
SRP007412_liver	0.04 RPM	81.27 RPM
SRP007412_testis	0.38 RPM	109.65 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_412 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_412 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_412 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_197

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Canis familiaris	ENSCAFG00000006884	1 retrocopy	retro_cfam_1339,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Macaca mulatta	ENSMMUG00000011125	4 retrocopies	retro_mmul_1242, retro_mmul_372, retro_mmul_417, retro_mmul_566,
Macaca mulatta	ENSMMUG00000013440	1 retrocopy	retro_mmul_387,
Macaca mulatta	ENSMMUG00000015010	1 retrocopy	retro_mmul_412 ,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,
Pongo abelii	ENSPPYG00000003512	1 retrocopy	retro_pabe_175,