RetrogeneDB ID: retro_pabe_203

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 15:56122388..56123534(+)
• Located in intron of: ENSPPYG00000006518

Retrocopy information

• Ensembl ID: ENSPPYG00000006520
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: LDHAL6A
• Ensembl ID: ENSPPYG00000003435
• Aliases: None
• Description: lactate dehydrogenase A-like 6A [Source:HGNC Symbol;Acc:28335]

Sequence

>retro_pabe_203
ATGAGTTGGACTGTGCCTGCTGTGCGGGCCAGCCAGAGAGTGAGCTCGGTGGGAGCGAATTTCCTATGCCTGGGGACGGC
CCTGTGTCCCCGTCAAGCAGCGCGCATCCCGCTCAAGGGCGCCTGGCTCTTCACCCCCGTGAGCAAGATGGCGACTGTGA
AGAGTGAGCTTATTGAGCGTTTCACTTCCGAGGAGCCCGTTCATCACAGTAAGGTCTCCATCATAGGAACTGGATCTGTG
GGCATGGCCTGCGCTATCAGCATCTTATTAAAAGGCTTGAGTGATGAACTTGCCCTTGTGGATCTTGATGAAGACAAACT
GAAGGGTGAGACAGTGGATCTTCAACATGGTAGCCCTTTCACGAAAATGCCAAATATTGTTTGTAGTAAAGATTACTTTG
TCACAGCGAACTCCAACCTAGTGATTATCACAGCAGGTGCACGCCAAGAAAAGGGAGAAACGCGCCTTAATTTAGTCCAG
CGAAATGTGGCCATCTTCAAGTTAATGATTTCCAGTATTGTCCAGTACAGCCCCCACTGCAAATTGATTATTGTTTCCAA
TCCAGTGGATATCTTAACCTATGTAGCTTGGAAGTTGAGTGCATTTCCCAAAAACCGTATTATTGGAAGCGGCTGTAATC
TGGATACTGCTCGTTTTCGTTTCTTGATTGGACAAAAGCTTGGTATCCATTCTGAAAGCTGCCATGGATGGATCCTTGGA
GAGCATGGAGACTCAAGTGTTCCTGTGTGGAGTGGAGTGAACATAGCTGGTGTCCCTTTGAAGGATCTGAACTCTGATAT
AGGAACTGATAAAGATCCTGAGCAATGGAAAAATGTCCACAAAGAAGTGATTGCTACTGCCTATGAGATTATTAAAATGA
AAGGTTATACTTCTTGGGCCATTGGCCTATCTGTGGCTGATTTAACAGAAAGTATTTTGAAGAATCTTAGGAGAATACAT
CCAGTTTCCACCATAATTAAGGGCCTCTATGGAATAGATGAAGAAGTATTCCTCAGTATTCCTTGTATCCTGGGAGAGAA
TGGTATTACCAACCTTATAAAGATAAAGCTGACCCCTGAAGAAGAGGCCCATCTGAAAAAAAGTGCAAAAACACTTTGGG
AAATTCAGAAGGAGCTTAAGCTTTAA

Alignment

ORF - retro_pabe_203 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.04 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATVKSELIKNFAEEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDVDEGKLKGETMDLQHGSP
          MATVKSELI..F..EE..HH.K.SI.GTGSVG.ACAISILLKGLSDEL.LVD.DE.KLKGET.DLQHGSP
Retrocopy MATVKSELIERFTSEEPVHHSKVSIIGTGSVGMACAISILLKGLSDELALVDLDEDKLKGETVDLQHGSP

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

Parental  DILTYVAWKLSAFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNIAGVP
          DILTYVAWKLSAFPKNR.IGSGCNLD.ARFR..IGQ.LGIHSESCHG.ILGEHGDSSVPVWSGVNIAGVP
Retrocopy DILTYVAWKLSAFPKNRIIGSGCNLDTARFRFLIGQKLGIHSESCHGWILGEHGDSSVPVWSGVNIAGVP

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

Parental  YGINEEIFLSVPCILGENGITDLIKVKLTFEEEACLQKSAETLWEIQKELKL
          YGI.EE.FLS.PCILGENGIT.LIK.KLT.EEEA.L.KSA.TLWEIQKELKL
Retrocopy YGIDEEVFLSIPCILGENGITNLIKIKLTPEEEAHLKKSAKTLWEIQKELKL

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	0.00 RPM	0.44 RPM
SRP007412_cerebellum	0.00 RPM	1.34 RPM
SRP007412_heart	0.00 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.30 RPM
SRP007412_liver	0.00 RPM	0.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_203 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_203 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_203 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_42
Pan troglodytes	retro_ptro_62
Macaca mulatta	retro_mmul_261
Callithrix jacchus	retro_cjac_164

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 24 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,
Pongo abelii	ENSPPYG00000003437	5 retrocopies	retro_pabe_2002, retro_pabe_2039, retro_pabe_2423, retro_pabe_3407, retro_pabe_364,
Pongo abelii	ENSPPYG00000004356	3 retrocopies	retro_pabe_1738, retro_pabe_1744, retro_pabe_3780,
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,