RetrogeneDB ID: retro_mmul_878

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 11:68874880..68875923(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRS2
• Ensembl ID: ENSMMUG00000001018
• Aliases: None
• Description: None

Sequence

>retro_mmul_878
CAGAGAAATGTTACTTCTTTTGAAGGGAAGAACACTGAGTTATACCAAGAGTTAGGTCTTCAAGCCAGAGATGTGAGATT
TCACCATGTAATGAGTATCACAGCCAGAAATAATAGGATTATCATGAGAATGGAGTATTTGAAAGCTGGGATAACTCGAG
AGTGTCTTCTGATTTTAGATTATCATAATTTAAACTCACAGCAATGGCTGTTCCGAGAACTCTCTTCACAATTGTCTGGA
GAGGGTCAACTTGTTATAAACCCTTTAACTTTTTGAGTTTAGAGCTATAGAAGCGCTCCCGCAATACCTGATCAACACCC
TTCAGGTGAAACTTAGCATTTTCCAGCCACTGATCCTCGAGACGTTGGAAGCTTTGGTGGACCCCAAACATTCTTCTGTA
GACAGAAGCAAACTCCACATTTTACTACAGAACAGCAAAAGTCTACTAGAGTTAGAAACAGATATTAAAATTTTCAAAGA
GTCAATCTTGGAGATTTTGGATGAGGAAGAGTTGCTAGAAGAGTTCTATCAAAATGGAGTGACCCACAAGTCTTTGAAAA
GAGCAGTACTGGGACTGACCATGCAGAGGAGATGGAGTTGCTGATGGAAAACTACCACCAACTGGCTGACGATCACTCCA
ATGCAGCTTAGGAGCTTAGGGTACTGATTGATGATTCACAAAGTATTATTTTCATCAATCCTGCCAGCCACCGTAACGTG
ATAATGAAGTTGAATCTACAGCTGACCGTAAGAACCTTCTCTCTTTTGCTCTTTGGAGTAATGGGAGTTGCTTTTGGAAT
GAGTTTGGAATCTCCCCTTGAAGAGGCCCAACGAGTGTTTTGGCTGATTACAGGAATTACGTTCATGGGAAGTGGCCTTA
TCTGGAGGCGCCCGCTTTCATTCCTGGGACAACAGCTAGAAGTTCCACTGCCTCGCATGACGGCCTCCTTACCTAAAAAG
ACTCTTCTAGCAGATACAAGCGTGGAACAAAAAACAGCCTCAGACCCGATGGACTTGGATCAGGCAGGAGTATCCTAACA
AAC

Alignment

ORF - retro_mmul_878 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.67 %
• Parental protein coverage: 78.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QGNVTSFEKKKTELYQELGLQARDLRFQHVMSITVRNNRIIMRMEYLKAVITPECLLILDYRNLNLEQWL
          Q.NVTSFE.K.TELYQELGLQARD.RF.HVMSIT.RNNRIIMRMEYLKA.IT.ECLLILDY.NLN..QWL
Retrocopy QRNVTSFEGKNTELYQELGLQARDVRFHHVMSITARNNRIIMRMEYLKAGITRECLLILDYHNLNSQQWL

Parental  FRELPSQLSGEGQLVTYPLPF-EFRAIEALLQYWINTLQGKLSILQPLILETLDALVDPKHSSVDRSKLH
          FREL.SQLSGEGQLV..PL.F.EFRAIEAL.QY.INTLQ.KLSI.QPLILETL.ALVDPKHSSVDRSKLH
Retrocopy FRELSSQLSGEGQLVINPLTF>EFRAIEALPQYLINTLQVKLSIFQPLILETLEALVDPKHSSVDRSKLH

Parental  ILLQNGKSLSELETDIKIFKESILEILDEEELLEE-LCLSKWSDPQVFEKSSAGIDHAEEMELLLENYYR
          ILLQN.KSL.ELETDIKIFKESILEILD.EE.L.E...LSKWSDPQVFEKSS.G.DHAEEMELL.ENY..
Retrocopy ILLQNSKSLLELETDIKIFKESILEILD-EEELLE<RVLSKWSDPQVFEKSSTGTDHAEEMELLMENYHQ

Parental  LADDLSNAARELRVLIDDSQSIIFINLDSHRNVMMRLNLQLTMGTFSLSLFGLMGVAFGMNLESSLEEDH
          LADD.SNAA.ELRVLIDDSQSIIFIN..SHRNV.M.LNLQLT..TFSL.LFG.MGVAFGM.LES.LEE..
Retrocopy LADDHSNAA*ELRVLIDDSQSIIFINPASHRNVIMKLNLQLTVRTFSLLLFGVMGVAFGMSLESPLEEAQ

Parental  RIFWLITGIMFMGSGLIWRRLLSFLGRQLEAPLPPMMAPLPKKTLLADRSVE-LKNSLRLDGLGSGRGIL
          R.FWLITGI.FMGSGLIWRR.LSFLG.QLE.PLP.M.A.LPKKTLLAD.SVE..KNSLR.DGLGSGR.IL
Retrocopy RVFWLITGITFMGSGLIWRRPLSFLGQQLEVPLPRMTASLPKKTLLADTSVE<TKNSLRPDGLGSGRSIL

Parental  TN
          TN
Retrocopy TN

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	4.82 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	5.32 RPM
SRP007412_cerebellum	0.19 RPM	8.27 RPM
SRP007412_heart	0.06 RPM	12.25 RPM
SRP007412_kidney	0.00 RPM	7.39 RPM
SRP007412_liver	0.04 RPM	3.29 RPM
SRP007412_testis	0.08 RPM	1.66 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_878 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_878 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_878 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_939

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000006424	1 retrocopy	retro_dnov_1486,
Equus caballus	ENSECAG00000013105	1 retrocopy	retro_ecab_1032,
Homo sapiens	ENSG00000124532	1 retrocopy	retro_hsap_4006,
Gorilla gorilla	ENSGGOG00000009098	1 retrocopy	retro_ggor_2689,
Macaca mulatta	ENSMMUG00000001018	2 retrocopies	retro_mmul_2312, retro_mmul_878 ,
Pongo abelii	ENSPPYG00000016278	1 retrocopy	retro_pabe_939,
Pan troglodytes	ENSPTRG00000017774	1 retrocopy	retro_ptro_2720,