RetrogeneDB ID: retro_pabe_779

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 11:79517045..79518032(-)
• Located in intron of: ENSPPYG00000003737

Retrocopy information

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

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_779
ATGGTAACTATCCAGAATGAATTTATTGAGAATTTTGCTTCAGAGGTGGTTATTCACCACAGTAAGGTCTCCATTATAAG
AACTGGATCAGTTAGCACGGCCAGTGCAATCACCATGTTTTTAAAAGACTTGAGGGATGAAGTTGCCTTTGTAGCTGTTG
ATAATGGTGAATTGAAGGGTGTGAGACAATGGATCTTAAACATGGCAATCTTTTCCTAAAACTGCCAAATAGTGCTTCCA
GCAAAGATTATCTCATCTCTGCGAACTCCAACCTAGTGATAATCACATCAAGTGCATGCCAGGAAAAAGGTGAAACACTT
TAATTTAGTCAGTCTAAATGTGGCCATCATTAAATTAATGATGTCTAATATTACTCAATATAGTCCTGCTGCAAATTGAT
AGTTTCCAGTCCAGTGGATATCTTAATCTATGTAGCTTAGAAATTGAGTACATTTTTCAAAACCCATATTATTGGAAATG
GCTGTAATCTGGACACTGCCCATTTCCATTTCTTGACTGTGCAAATGCTTGGAATCCACTCTGGAAGCTGCCATGGGTTA
ATCTTTGGAGAGCATGGGGACTCAAGTGTTCCTATGTGGAGTGGAGTCAACATTGCTGGTGTCCCTCTGAAGGATCTGAA
TTCAGATAAAGGAATTGATCAAGATCTAGAGCAAGGGGGAAAATGTCCACAAAGAAGTGATTGCCAGTGCTTATGAAATT
ATGAAAATGAAAGATTATACTTCTTGGGCCATTGGCCCATCTGTAACTGATTGAACAGAAAGTATTTTAGAGAATCCTAG
GAGAGTGCATTCAGTTTCCACATAATTAAGGGCCTCTATGGAATGAATGAAGTATTCCTCAGTGTTCCTTGTATCTGAGA
GAGAATGGTCTTGCAGACCTTACATAGGTAAAGCTGACCCTTGAAGATGCAGCCCATTTGTGAAGGAGCACAGAAACACT
TTGGGAATTCAGAAGAAGCTCAAGCTT

Alignment

ORF - retro_pabe_779 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.12 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 4
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MATVKSELIKNFAEEEAIHHNKISIVGTGSVGVACAISILLKGLSDELVLVDVDEGK-LKG-ETMDLQHG
          M.T...E.I.NFA.E..IHH.K.SI..TGSV..A.AI...LK.L.DE...V.VD.G....G.ETMDL.HG
Retrocopy MVTIQNEFIENFASEVVIHHSKVSIIRTGSVSTASAITMFLKDLRDEVAFVAVDNGE<IEGCETMDLKHG

Parental  SPFMKMPNIVSSKDYLVTANSNLVIITAGARQ-KKGETRLDLVQRNVSIFKLMIPNITQYSPH-CKLLIV
          ..F.K.PN..SSKDYL..ANSNLVIIT..A.Q.KK......LV..NV.I.KLM..NITQYSP..CKL.IV
Retrocopy NLFLKLPNSASSKDYLISANSNLVIITSSACQ>KKVK-HFNLVSLNVAIIKLMMSNITQYSPA<CKL-IV

Parental  TNPVDILTYVAWKLSAFPKNRVIGSGCNLDSARFRYFIGQRLGIHSESCHGLILGEHGDSSVPVWSGVNI
          ..PVDIL.YVA.KLS.F.K...IG.GCNLD.A.F.....Q.LGIHS.SCHGLI.GEHGDSSVP.WSGVNI
Retrocopy SSPVDILIYVA*KLSTFFKTHIIGNGCNLDTAHFHFLTVQMLGIHSGSCHGLIFGEHGDSSVPMWSGVNI

Parental  AGVPLKDLNPDIGTDKDPEQ-WENVHKKVISSGYEMVKMKGYTSWGISLSVADLTESILKNLRRVHPVST
          AGVPLKDLN.D.G.D.D.EQ..ENVHK.VI.S.YE..KMK.YTSW.I..SV.D.TESIL.N.RRVH.VST
Retrocopy AGVPLKDLNSDKGIDQDLEQ>GENVHKEVIASAYEIMKMKDYTSWAIGPSVTD*TESILENPRRVHSVST

Parental  -LSKGLYGINEEIFLSVPCI-LGENGITDLIKVKLTFEEEACLQKSAETLWE-IQKELKL
          ...KGLYG.N.E.FLSVPCI.L.ENG..DL..VKLT.E..A.L..S.ETLWE.IQK.LKL
Retrocopy <IIKGLYGMN-EVFLSVPCI<LRENGLADLT*VKLTLEDAAHL*RSTETLWE<IQKKLKL

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	0.06 RPM	0.44 RPM
SRP007412_cerebellum	0.00 RPM	1.34 RPM
SRP007412_heart	0.06 RPM	0.12 RPM
SRP007412_kidney	0.00 RPM	0.30 RPM
SRP007412_liver	0.06 RPM	0.28 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_779 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_779 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_779 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_905
Macaca mulatta	retro_mmul_1111
Equus caballus	retro_ecab_933

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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,