RetrogeneDB ID: retro_ptro_1369

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 19:42335477..42336380(-)
• Located in intron of: ENSPTRG00000010893

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACOT4
• Ensembl ID: ENSPTRG00000006518
• Aliases: None
• Description: acyl-CoA thioesterase 4 [Source:HGNC Symbol;Acc:19748]

Sequence

>retro_ptro_1369
CGCGCGTCCCTGCGCGGCGAGAAGGGTGGGCTCTTCCGCTACTGCGCCGACGCCCGCGGCGAGCTGGACCTGGAGCGCGC
GCCCGTGCTGGGCGGCAGCTTTAGGGGGCTAGAGTCCATGGGGCTGCTCTGGGCCCTGGAATCCAAGAAACCTTTTTGGC
ACTTTCTGAAGCGGGACGTACAGATTCCCTTTATCGTGGAGTCGGAGGTGCTGGACGGCCACGACCCCGAGCCTGGACGG
CTGTTGTGACAGGCGCGGCACGAGGGCGACTTCCTCCCACAGGGGGTGCGGCGCGATTCGGTGCGCGCGGGCCGGGTGCG
CGCCACGCTCTTCCTGCCGCCAGGACCTGGACCCTTCCTAGGGATCATTGGCATCTTTGGTATTGGAGGGAGCCTGTTGG
AATATCGAGCCAGCCTCCTTGCTGGCCATGGCTTTGCCACGTTCGCTCTAGCTTGTTATAACTTTGAAGATCTCCCCAAG
AACGTGGACAACATACCCCTGGAGTACTTCGAAGAAGCCCTATGCTACATGCTTCAACATCCCCAGGTAAAAGGCCCAGG
CACTGGGCTTTGGGGCATTTCTCTAGGAGCTGATATTTGTCTCTCAATGGCCTCATTCTTGAAGAATGACTCAGACACAG
TTTCCATCAATGGATCCGGGATCAGTGGGAACAGAGGCATAAACTGTAAGCAGAATAGCATTCCACCATTGGGCTATGAC
CTGAGGAGAATCAAGGTAGCTTTCTCAGGCCTCGTGGACGTCGTGGATATAAAGAATGATCTTGTAGGAGGGTATGAGAA
CCCCAGCATGATTTCAATGGAGAAGGCCCAGGGCCCCATCCTTTTCATTGTTGGTCAGGATGACCATAACTGGAGGAGTG
AGTTGTATGCCCAGTCTCTGAAC

Alignment

ORF - retro_ptro_1369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.26 %
• Parental protein coverage: 72.45 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RASLRDEKGALFRAHARYCADARGELDLERAPALGGSFAGLEPMGLLWALEPEKPFWRFLKRDVQIPFVV
          RASLR.EKG.LF....RYCADARGELDLERAP.LGGSF.GLE.MGLLWALE..KPFW.FLKRDVQIPF.V
Retrocopy RASLRGEKGGLF----RYCADARGELDLERAPVLGGSFRGLESMGLLWALESKKPFWHFLKRDVQIPFIV

Parental  ELEVLDGHDPEPGRLLCQAQHERHFLPPGVRRQSVRAGRVRATLFLPPGPGPFPGIIDIFGIGGGLLEYR
          E.EVLDGHDPEPGRLL.QA.HE..FLP.GVRR.SVRAGRVRATLFLPPGPGPF.GII.IFGIGG.LLEYR
Retrocopy ESEVLDGHDPEPGRLL*QARHEGDFLPQGVRRDSVRAGRVRATLFLPPGPGPFLGIIGIFGIGGSLLEYR

Parental  ASLLAGHGFATLALAYYNFEDLPNNMDNISLEYFEEAVCYMLQHPQVKGPGIGLLGISLGADICLSMASF
          ASLLAGHGFAT.ALA.YNFEDLP.N.DNI.LEYFEEA.CYMLQHPQVKGPG.GL.GISLGADICLSMASF
Retrocopy ASLLAGHGFATFALACYNFEDLPKNVDNIPLEYFEEALCYMLQHPQVKGPGTGLWGISLGADICLSMASF

Parental  LKNVSATVSINGSGISGNTAINYKHSSIPPLGYDLRRIKVAFSGLVDIVDIRNALVGGYKNPSMIPIEKA
          LKN.S.TVSINGSGISGN..IN.K..SIPPLGYDLRRIKVAFSGLVD.VDI.N.LVGGY.NPSMI..EKA
Retrocopy LKNDSDTVSINGSGISGNRGINCKQNSIPPLGYDLRRIKVAFSGLVDVVDIKNDLVGGYENPSMISMEKA

Parental  QGPILLIVGQDDHNWRSELYAQTVS
          QGPIL.IVGQDDHNWRSELYAQ...
Retrocopy QGPILFIVGQDDHNWRSELYAQSLN

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	0.20 RPM	1.57 RPM
SRP007412_cerebellum	0.04 RPM	2.04 RPM
SRP007412_heart	0.03 RPM	0.29 RPM
SRP007412_kidney	0.03 RPM	9.70 RPM
SRP007412_liver	0.00 RPM	19.38 RPM
SRP007412_testis	0.11 RPM	0.95 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1369 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1369 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1369 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_1638

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000177465	1 retrocopy	retro_hsap_1997,
Macaca mulatta	ENSMMUG00000006856	1 retrocopy	retro_mmul_1376,
Nomascus leucogenys	ENSNLEG00000016052	1 retrocopy	retro_nleu_897,
Pongo abelii	ENSPPYG00000029617	1 retrocopy	retro_pabe_1638,
Pan troglodytes	ENSPTRG00000006518	1 retrocopy	retro_ptro_1369 ,