RetrogeneDB ID: retro_mmul_1111

Retrocopy location

• Organism: Rhesus macaque (Macaca mulatta)
• Coordinates: 14:82084490..82085477(-)
• Located in intron of: ENSMMUG00000007921

Retrocopy information

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

Parental gene information

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

Sequence

>retro_mmul_1111
ATGGTAACTATCCAGAATGAATTTATTGAGAATTTTGCTTCAGAGGAGGTTATTAACCACAGTAAGGTCTCCATTATAAG
AACTGGATCAGTTAGCATGGCCCATGCGGTCACCATGTTATTAAAAGACTTGAGGGATTAACTTGCCTTTGTAGATGTTG
ATAATGGTGAATTGAAGGGTGTGAGACAATGGATCTTAAACAAGGCAGTCTTTTCTTGAAACTGCCAAATAGTGTTTCCA
GCAAAGATTATCTCATCTCTGCAAACTCCAACCTAGTGATTATCACATCAGGTGCATGCCAGGAAAAAGGTGAAACACTT
TAATTTGGTCAGTCTAAATGTGGCCATCTTTAAATTAATGATTTCTAATATTACCCAATATAGTCCTGCTGCAAACTGAT
AGTTTCCAGTCCAGTGGATATCTTAAGTTATGTAGCTTGGAAGTTGAGTACATTTTCCAAAACCCATATTATTGGAAATG
GCTATAATCTGGACACTGCCTATTTCCATTTCTTGACTGTGCAAATGCTTGGAATCCACTCTGGAAGCTGCCATGGGTGG
ATCTTTGGAGAGCATAGGGACTCAAATGTTCCTGTGTGGAGTGCAGTGAACATTACTGGTATCCCTCTGAAGGATCTGAA
CTCAGATAGAGGAATTAATCAAAATCTGGAGCAAGGGGGAAAATGTCCACAAAGAAGTGATTGCCAGTGCCTATGAAATT
ATGAAAATGAAAGGTTATACTTCTTGGGCCATTGGCCCATCTGTAACTGATTGAACGGAAAGTATTTTAGGGAATCCAAG
GAGAGTACATTCAGTTTCCACATAATTAAGAGCCTCTGTGGAATGAATGAAGTATTCCTCAATGTTCCTTGTATCTAAGA
GAGAATGGTCTTGCAGACCTTACACAGGTAAAGCTGACCCTTGAAGAGGCGGCCCATTTGTAAAGGAGCACTTTACAAAC
ACTTTCGGAATTCAGAAGAAGCTCAAG

Alignment

ORF - retro_mmul_1111 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.06 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MATVKSELIKNFTKEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDADEGK-LKG-ETMDLQHG
          M.T...E.I.NF..EE.I.H.K.SI..TGSV..A.A...LLK.L.D.L..VD.D.G....G.ETMDL..G
Retrocopy MVTIQNEFIENFASEEVINHSKVSIIRTGSVSMAHAVTMLLKDLRD*LAFVDVDNGE<IEGCETMDLKQG

Parental  SPFMKMPNIVSSKDYLVTANSNLVIITAGARQ-KKGETRLDLVQRNVSIFKLMIPNITQYSPH-CKLLIV
          S.F.K.PN.VSSKDYL..ANSNLVIIT.GA.Q.KK......LV..NV.IFKLMI.NITQYSP..CKL.IV
Retrocopy SLFLKLPNSVSSKDYLISANSNLVIITSGACQ>KKVK-HFNLVSLNVAIFKLMISNITQYSPA<CKL-IV

Parental  TNPVDILTYVAWKLSAFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNI
          ..PVDIL.YVAWKLS.F.K...IG.G.NLD.A.F.....Q.LGIHS.SCHG.I.GEH.DS.VPVWS.VNI
Retrocopy SSPVDILSYVAWKLSTFSKTHIIGNGYNLDTAYFHFLTVQMLGIHSGSCHGWIFGEHRDSNVPVWSAVNI

Parental  AGVPLKDLNPDIGTDKDPEQ-WENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVST
          .G.PLKDLN.D.G.....EQ..ENVHK.VI.S.YE..KMKGYTSW.I..SV.D.TESIL.N.RRVH.VST
Retrocopy TGIPLKDLNSDRGINQNLEQ>GENVHKEVIASAYEIMKMKGYTSWAIGPSVTD*TESILGNPRRVHSVST

Parental  -LSKGLYGINEEIFLSVPCI-LGENGITDLIKVKLTLEEEACLQKSA-ETLWE-IQKELK
          ...K.L.G.N.E.FL.VPCI.L.ENG..DL..VKLTLEE.A.L..S...TL.E.IQK.LK
Retrocopy <IIKSLCGMN-EVFLNVPCI<LRENGLADLTQVKLTLEEAAHL*RSTLQTLSE<IQKKLK

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	0.00 RPM	0.18 RPM
SRP007412_kidney	0.00 RPM	0.12 RPM
SRP007412_liver	0.00 RPM	0.00 RPM
SRP007412_testis	0.00 RPM	0.26 RPM

ChIP-Seq

Macaca mulatta was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_mmul_1111 retrocopy.

TSS

Macaca mulatta was not studied using FANTOM5 data.

Lab

retro_mmul_1111 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmul_1111 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_905
Pongo abelii	retro_pabe_779
Equus caballus	retro_ecab_933

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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,