RetrogeneDB ID: retro_ptro_62

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 15:56556551..56557697(+)
• Located in intron of: ENSPTRG00000007124

Retrocopy information

• Ensembl ID: ENSPTRG00000007125
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSPTRG00000003423
• Aliases: None
• Description: lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]

Sequence

>retro_ptro_62
ATGAGTTGGACTGTGCCTGTTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAATTTCCCATGCCTGGGGATGGC
CCTGTGTCCGCGTCAAGCAACGCGCATCCCGCTCAACGGCACCTGGCTCTTCACCCCCGTGAGCAAGATGGCGACTGTGA
AGAGTGAGCTTATTGAGCGTTTCACTTCCGAGAAGCCCGTTCATCACAGTAAGGTCTCCATCATAGGAACTGGATCGGTG
GGCATGGCCTGCGCTATCAGCATCTTATTAAAAGGCTTGAGTGATGAACTTGCCCTTGTGGATCTTGATGAAGACAAACT
GAAGGGTGAGACAATGGATCTTCAACATGGCAGCCCTTTCACGAAAATGCCAAATATTGTTTGTAGCAAAGATTACTTTG
TCACAGCAAACTCCAACCTAGTGATTATCACAGCAGGTGCACGCCAAGAAAAGGGAGAAACGCGCCTTAATTTAGTCCAG
CGAAATGTGGCCATCTTCAAGTTAATGATTTCCAGTATTGTCCAGTACAGCCCCCACTGCAAACTGATTATTGTTTCCAA
TCCAGTGGATATCTTAACTTATGTAGCTTGGAAGTTGAGTGCATTTCCCAAAAACCGTATTATTGGAAGCGGCTGTAATC
TGGATACTGCTCGTTTTCGTTTCTTGATTGGACAAAAGCTTGGTATCCATTCTGAAAGCTGCCATGGATGGATCCTCGGA
GAGCATGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATAGCTGGTGTCCCTTTGAAGGATCTGAACTCTGATAT
AGGAACTGATAAAGATCCTGAGCAATGGAAAAATGTCCACAAAGAAGTGATTGCAACTGCCTATGAGATTATTAAAATGA
AAGGTTATACTTCTTGGGCCATTGGCCTATCTGTGGCCGATTTAACAGAAAGTATTCTGAAGAATCTTAGGAGAATACAT
CCAGTTTCCACCATAATTAAGGGCCTCTATGGAATAGATGAAGAAGTATTCCTCAGTATTCCTTGTATCCTGGGAGAGAA
CGGTATTACCAACCTTATAAAGATAAAGCTGACCCCTGAAGAAGAGGCCCATCTGAAAAAAAGTGCAAAAACACTTTGGG
AAATTCAGAATAAGCTTAAGCTTTAA

Alignment

ORF - retro_ptro_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.53 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATIKSELIKNFAEEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDVDEGKLKGETMDLQHGSP
          MAT.KSELI..F..E...HH.K.SI.GTGSVG.ACAISILLKGLSDEL.LVD.DE.KLKGETMDLQHGSP
Retrocopy MATVKSELIERFTSEKPVHHSKVSIIGTGSVGMACAISILLKGLSDELALVDLDEDKLKGETMDLQHGSP

Parental  FMKMPNIVSSKDYLVTANSNLVIITAGARQKKGETRLDLVQRNVSIFKLMIPNITQYSPHCKLLIVTNPV
          F.KMPNIV.SKDY.VTANSNLVIITAGARQ.KGETRL.LVQRNV.IFKLMI..I.QYSPHCKL.IV.NPV
Retrocopy FTKMPNIVCSKDYFVTANSNLVIITAGARQEKGETRLNLVQRNVAIFKLMISSIVQYSPHCKLIIVSNPV

Parental  DILTYVAWKLSGFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNIAGVP
          DILTYVAWKLS.FPKNR.IGSGCNLD.ARFR..IGQ.LGIHSESCHG.ILGEHGDSSVPVWSGVNIAGVP
Retrocopy DILTYVAWKLSAFPKNRIIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP

Parental  LKDLNPDIGTDKDPEQWENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVSTLSKGL
          LKDLN.DIGTDKDPEQW.NVHK.VI...YE..KMKGYTSW.I.LSVADLTESILKNLRR.HPVST..KGL
Retrocopy LKDLNSDIGTDKDPEQWKNVHKEVIATAYEIIKMKGYTSWAIGLSVADLTESILKNLRRIHPVSTIIKGL

Parental  YGINEDIFLSVPCILGENGITDLIKVKLTLEEEACLQKSAETLWEIQKELKL
          YGI.E..FLS.PCILGENGIT.LIK.KLT.EEEA.L.KSA.TLWEIQ..LKL
Retrocopy YGIDEEVFLSIPCILGENGITNLIKIKLTPEEEAHLKKSAKTLWEIQNKLKL

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_prefrontal_cortex	0.02 RPM	1.91 RPM
SRP007412_cerebellum	0.00 RPM	2.90 RPM
SRP007412_heart	0.09 RPM	0.61 RPM
SRP007412_kidney	0.24 RPM	0.65 RPM
SRP007412_liver	0.03 RPM	0.07 RPM
SRP007412_testis	47.74 RPM	2.11 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_62 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_62 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_42
Pongo abelii	retro_pabe_203
Macaca mulatta	retro_mmul_261
Callithrix jacchus	retro_cjac_164

---

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	ENSMMUG00000014614	2 retrocopies	retro_mmul_1111, retro_mmul_261,
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	ENSPTRG00000003421	5 retrocopies	retro_ptro_1540, retro_ptro_1618, retro_ptro_2039, retro_ptro_259, retro_ptro_2875,
Pan troglodytes	ENSPTRG00000003423	1 retrocopy	retro_ptro_62 ,
Pan troglodytes	ENSPTRG00000004762	1 retrocopy	retro_ptro_3237,
Tarsius syrichta	ENSTSYG00000008062	4 retrocopies	retro_tsyr_1811, retro_tsyr_2064, retro_tsyr_2071, retro_tsyr_731,