RetrogeneDB ID: retro_pabe_1638

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:37239840..37240752(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ACOT4
• Ensembl ID: ENSPPYG00000029617
• Aliases: None
• Description: acyl-CoA thioesterase 4 [Source:HGNC Symbol;Acc:19748]

Sequence

>retro_pabe_1638
CGCGCGTCCCTGCGCGACGAGAAGGGTGGGCTCTTCCGGGCCCACGCGCGCTACTGCGCCGACGCCCGCGGCGAGCTGGA
CCTGGAGCGCGCGCCCGTGCTGGGCGGCAGCTTCGTGGGGCTCGAGTCCATGGGGCTGCTGTGGGCCATGGAATCCAAGA
AGCCTTTTTGGCGCTTTCTGAAGCGGGAGGTACAGATTCCCTTTATCGTGGAGTTGGAGGTGCTGGACGGCCACGACCCC
GAGCCTGGACGGCTGTTGTGACAGGCGCGGCACGAGCGCGACTTCCTCCCGCAGGGGGTGCGGCGCGATTCGGTGCGCGC
GGGCCGGGTGCGCGCCACGCTCTTCCTGCCGCCAGGACCTGGACCCTTCCTAGGGATCACTGGCATCTTTGGTATTGGAG
GGAGCCTGTTGGAATATCGAGCCAGCCTCCCTGCTGGCCATGGCTTTGCCATGTTCGCTCTAGCTTATTATAACTTTGAA
GATCTCTGCAAGAACGTGGACAACATACCCCTGGAGTACTTCGAAGAAGCCCTATGCTACATGCGTCAACATCCCCAGGT
AAAAGGCCCAGGCATTGGGCCTTGGGGCATTTCTCTAGGAGCTGATATTTGTCTCTCAATGGCCTCATTCTTGAAGAATG
ACTCAGACACAGTTTCCATCAATGGATCCGGGATCAGTGGGAACAGAGGCATAAACTATAAGCAGAATAGCATTCCACCG
TTGGGCTATGACCTGAGGAGAATCAGGGTAGCTTTCTCAGGCCTCGTGGACATCGTGGATATAAGGAATGATCTTGTAGG
AGGGTATGAGAACCCCAGCATGATTTCAGTAGAGAAGGCCCAGGGCCCCATCCTTTTCATTGTTGGTCAGGATGACCATA
ACTGGAAGAGTGAGTTGTATGCCCAGTCTCTG

Alignment

ORF - retro_pabe_1638 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.17 %
• Parental protein coverage: 72.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RASLRDEKGALFRAHARYCADARGELDLERAPALGGSFAGLEPMGLLWALEPEKPFWRFLKRDVQIPFVV
          RASLRDEKG.LFRAHARYCADARGELDLERAP.LGGSF.GLE.MGLLWA.E..KPFWRFLKR.VQIPF.V
Retrocopy RASLRDEKGGLFRAHARYCADARGELDLERAPVLGGSFVGLESMGLLWAMESKKPFWRFLKREVQIPFIV

Parental  ALEVLDGHDPEPGRLLCQARHERHFLPQGVRRQSVRAGRVRATLFLPPGPGPFPGIIDIFGIGGGLLEYR
          .LEVLDGHDPEPGRLL.QARHER.FLPQGVRR.SVRAGRVRATLFLPPGPGPF.GI..IFGIGG.LLEYR
Retrocopy ELEVLDGHDPEPGRLL*QARHERDFLPQGVRRDSVRAGRVRATLFLPPGPGPFLGITGIFGIGGSLLEYR

Parental  ASLLAGHGFATLALAYYNFEDLPNNMDNISLEYFEEALCYMLQHPQVKGPGIGLLGISLGADICLSMASF
          ASL.AGHGFA..ALAYYNFEDL..N.DNI.LEYFEEALCYM.QHPQVKGPGIG..GISLGADICLSMASF
Retrocopy ASLPAGHGFAMFALAYYNFEDLCKNVDNIPLEYFEEALCYMRQHPQVKGPGIGPWGISLGADICLSMASF

Parental  LKNVSATVSINGSGISGNTAINYKHNSIPPLGYDLRRIKVAFSGLVDIVDIRNALVGGYENPSMIPVEKA
          LKN.S.TVSINGSGISGN..INYK.NSIPPLGYDLRRI.VAFSGLVDIVDIRN.LVGGYENPSMI.VEKA
Retrocopy LKNDSDTVSINGSGISGNRGINYKQNSIPPLGYDLRRIRVAFSGLVDIVDIRNDLVGGYENPSMISVEKA

Parental  QGPILLIVGQDDHNWRSELYAQTV
          QGPIL.IVGQDDHNW.SELYAQ..
Retrocopy QGPILFIVGQDDHNWKSELYAQSL

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	0.77 RPM	1.16 RPM
SRP007412_cerebellum	0.73 RPM	2.19 RPM
SRP007412_heart	0.06 RPM	0.33 RPM
SRP007412_kidney	0.03 RPM	5.67 RPM
SRP007412_liver	0.00 RPM	12.70 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1638 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1638 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1638 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_1369

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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,