RetrogeneDB ID: retro_mmul_261

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 7:37578884..37580030(+)
• Located in intron of: ENSMMUG00000012933

Retrocopy information

• Ensembl ID: ENSMMUG00000012934
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSMMUG00000014614
• Aliases: None
• Description: L-lactate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F7GNJ6]

Sequence

>retro_mmul_261
ATGAGTTGGACTGTGCCTCTTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAATTTCCTGTGCCTGAAGATGGC
CCTGTGTCCCCGTCAGGCAGCGCGCATCCCACTCAAGGGCGCCTGGCGCTTCACCTCCGTGAGCAAGATGGCGACTGTGA
AGAGTGAGCTTATTGAGCGCTTCACTTCTGAGGAGCCCGTTCATCACAGTAAGGTCTCCATCATAGGAACTGGATCGGTG
GGCATGGCCTGCGCTATCAGCATCTTATTAAAAGGCTTGATCGATGAACTTGCCCTTGTGGATGTTGATGAAGGCAAACT
GAAGGGTGAGACGATGGATCTTCAACATGGCAGCTCTTTCACGAAAATGCCAAATATTGTTTGTAGCAAAGATTACATTG
TCACCGCAAACTCCAACCTAGTGATTATCACAGCAGGTGCACGCCAAGAAAAGGGAGAAACGCGCCTTAATTTAGTGCAG
CGAAATGTGGCCCTCTTCAAGTTAATGATTTCCAATATTGTCCAGCATAGTCCCCACTGCAAACTGATTATTGTTTCCAA
TCCAGTGGATATCTTAAGTTATGTAGCTTGGAAGCTGAGTGCATTTCCCAAAAACCGTGTTATTGGAAGCGGCTGTAACC
TGGATACCGCTCGTTTTCGTTTCTTGATTGGACAAAAGCTTGGTATCCATTCTGAAAGCTGCCATGGATGGATCCTCGGA
GAGCACGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATAGCTGGTGTCCCTTTGAAGGACCTGAACTCTGATAT
AGGAACTGATAAAGATCCTGAGCAATGGAAAAATGTCCACGAAGAAGTGATTGCTACTGCCTATGAGATTATTAAAATGA
AAGGTTATACTTCTTGGGCCATTGGCCTATCTGTGGCTGATTTAACAGAAAGTATTTTGAAGAATCTTAGGAGAACACAT
CCAGTTTCCACCATAATTAAGGGCCTCTATGGAATAGATGAAGAAGTATTCCTCAGTATTCCTTGTATCCTGGGAGAGAA
TGGTATTACCCATCTTATAAAGATAAAGCTGACCCCTGAAGAAGAGGACCGTCTGAAAAAAAGTGCAAAAACACTTTGGG
AAATTCAGAAGGAGCTCAAGATTTAA

Alignment

ORF - retro_mmul_261 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.38 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATVKSELIKNFTKEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDADEGKLKGETMDLQHGSP
          MATVKSELI..FT.EE..HH.K.SI.GTGSVG.ACAISILLKGL.DEL.LVD.DEGKLKGETMDLQHGS.
Retrocopy MATVKSELIERFTSEEPVHHSKVSIIGTGSVGMACAISILLKGLIDELALVDVDEGKLKGETMDLQHGSS

Parental  FMKMPNIVSSKDYLVTANSNLVIITAGARQKKGETRLDLVQRNVSIFKLMIPNITQYSPHCKLLIVTNPV
          F.KMPNIV.SKDY.VTANSNLVIITAGARQ.KGETRL.LVQRNV..FKLMI.NI.Q.SPHCKL.IV.NPV
Retrocopy FTKMPNIVCSKDYIVTANSNLVIITAGARQEKGETRLNLVQRNVALFKLMISNIVQHSPHCKLIIVSNPV

Parental  DILTYVAWKLSAFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNIAGVP
          DIL.YVAWKLSAFPKNRVIGSGCNLD.ARFR..IGQ.LGIHSESCHG.ILGEHGDSSVPVWSGVNIAGVP
Retrocopy DILSYVAWKLSAFPKNRVIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP

Parental  LKDLNPDIGTDKDPEQWENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVSTLSKGL
          LKDLN.DIGTDKDPEQW.NVH..VI...YE..KMKGYTSW.I.LSVADLTESILKNLRR.HPVST..KGL
Retrocopy LKDLNSDIGTDKDPEQWKNVHEEVIATAYEIIKMKGYTSWAIGLSVADLTESILKNLRRTHPVSTIIKGL

Parental  YGINEEIFLSVPCILGENGITDLIKVKLTLEEEACLQKSAETLWEIQKELK
          YGI.EE.FLS.PCILGENGIT.LIK.KLT.EEE..L.KSA.TLWEIQKELK
Retrocopy YGIDEEVFLSIPCILGENGITHLIKIKLTPEEEDRLKKSAKTLWEIQKELK

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	0.11 RPM
SRP007412_brain_prefrontal_cortex	0.00 RPM	0.00 RPM
SRP007412_cerebellum	0.00 RPM	0.13 RPM
SRP007412_heart	0.12 RPM	0.18 RPM
SRP007412_kidney	0.35 RPM	0.12 RPM
SRP007412_liver	0.08 RPM	0.00 RPM
SRP007412_testis	45.61 RPM	0.26 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_261 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_261 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_261 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_42
Pan troglodytes	retro_ptro_62
Pongo abelii	retro_pabe_203
Callithrix jacchus	retro_cjac_164

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007067	2 retrocopies	retro_cjac_164, retro_cjac_2180,
Homo sapiens	ENSG00000166800	2 retrocopies	retro_hsap_42, retro_hsap_905,
Macaca mulatta	ENSMMUG00000002679	4 retrocopies	retro_mmul_212, retro_mmul_303, retro_mmul_308, retro_mmul_315,
Macaca mulatta	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261 ,
Macaca mulatta	ENSMMUG00000031024	2 retrocopies	retro_mmul_1037, retro_mmul_587,
Nomascus leucogenys	ENSNLEG00000017780	2 retrocopies	retro_nleu_29, retro_nleu_378,
Otolemur garnettii	ENSOGAG00000009261	1 retrocopy	retro_ogar_2662,
Pongo abelii	ENSPPYG00000003435	2 retrocopies	retro_pabe_203, retro_pabe_779,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,