RetrogeneDB ID: retro_ptro_2016

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:130666427..130667231(+)
• Located in intron of: ENSPTRG00000016437

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOSL1
• Ensembl ID: ENSPTRG00000003901
• Aliases: None
• Description: FOS-like antigen 1 [Source:HGNC Symbol;Acc:13718]

Sequence

>retro_ptro_2016
GACTTCAGGGAACCCGGCCCGAGCTCCGGGAATGGCGTGGGTATGGCGACCCCGCGCAGCCCCCCGGCCGCAGTGCAGGC
AGCCCAGCAGAAGTTCCACCTCGTGCCAAGGATCAACAACATGAGTGGCAGTCAGGAGCTGCAGTGGATGGTACAGCCTC
ATTTTCTGGGGCCCAGCAGTTGCCCCAGGCCTCTGACCTACCCTTAGTCCAGCCCCCTACAACCCCAGCCAGGAGTCATC
CGGGCCCTGGGGCCGCCTCCAGGGGTATGTCCAAAGCCTTGCGAACAGATCAGCCCGGAGGAAGAGGAGCGCCGCCGAGT
AAGGCCCGAGCGGAACAAGCTGGCTGCGGCCAAGTGTAGGAACTGGAGGAAGGAACTGACTGACTTCCTGCAGGCGGAGA
CTGATAAACTGGAAGATGAGAAATCCGGGCTGCAGCGAGAGATCGAGGAGCTGCAGAAGCAGAAGGAGCGCCTGGAGCTG
GTGCTGGAAGCCCACTGACCCATCTGCAAAATCCCCGAAGGAGCCAAGGAGGGATACACAGGCGGTACCAGCGGCACCAG
CAGCCCGCCAGCCCCCTGCCTCCCTGTACCTTCTATCTCCCTTTCCCCAGGGCCTGTGCTTGAACCTGAGGCACTGCACA
CCCCCAAGCTCATGACCACACTCTCCCTAACTCCTTTCGCCCCCAGCCTGGTCTTCACGTACCCCAGCACTCCTGAGCCC
TGTGCCTCAGCTCATCACAAGAGTAGCAGCAGCAGCGGAGACCCATCCTCTGACCCCCTTGGCTCTCCAACCCTCCTCGC
TTTG

Alignment

ORF - retro_ptro_2016 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.81 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DFGEPGPSSGNGGGYGGQEQPPAAAQAAQQKFHLVPSINTMSGSQELQWMVQPHFLGPSSYPRPLTYPQY
          DF.EPGPSSGNG.G......PPAA.QAAQQKFHLVP.IN.MSGSQELQWMVQPHFLGPSS.PRPLTYP..
Retrocopy DFREPGPSSGNGVGMATPRSPPAAVQAAQQKFHLVPRINNMSGSQELQWMVQPHFLGPSSCPRPLTYP*S

Parental  SPPQPRPGVIRALGPPPGVRRRPCEQISPEEEERRRVRRERNKLAAAKCRNRRKELTDFLQAETDKLEDE
          SP.QP.PGVIRALGPPPGV...PCEQISPEEEERRRVR.ERNKLAAAKCRN.RKELTDFLQAETDKLEDE
Retrocopy SPLQPQPGVIRALGPPPGVCPKPCEQISPEEEERRRVRPERNKLAAAKCRNWRKELTDFLQAETDKLEDE

Parental  KSGLQREIEELQKQKERLELVLEAHRPICKIPEGAKEGDTGSTSGTSSPPAPCRPVPCISLSPGPVLEPE
          KSGLQREIEELQKQKERLELVLEAH.PICKIPEGAKEG.TG.TSGTSSPPAPC.PVP.ISLSPGPVLEPE
Retrocopy KSGLQREIEELQKQKERLELVLEAH*PICKIPEGAKEGYTGGTSGTSSPPAPCLPVPSISLSPGPVLEPE

Parental  ALHTPTLMTTPSLTPFTPSLVFTYPSTPEPCASAHRKSSSSSGDPSSDPLGSPTLLAL
          ALHTP.LMTT.SLTPF.PSLVFTYPSTPEPCASAH.KSSSSSGDPSSDPLGSPTLLAL
Retrocopy ALHTPKLMTTLSLTPFAPSLVFTYPSTPEPCASAHHKSSSSSGDPSSDPLGSPTLLAL

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	0.13 RPM	0.39 RPM
SRP007412_cerebellum	0.04 RPM	0.54 RPM
SRP007412_heart	0.03 RPM	0.38 RPM
SRP007412_kidney	0.21 RPM	0.44 RPM
SRP007412_liver	0.69 RPM	4.45 RPM
SRP007412_testis	0.00 RPM	1.37 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2016 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2016 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2016 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2981
Pongo abelii	retro_pabe_2471
Macaca mulatta	retro_mmul_1904

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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	ENSG00000175592	1 retrocopy	retro_hsap_2981,
Macaca mulatta	ENSMMUG00000008653	1 retrocopy	retro_mmul_1904,
Nomascus leucogenys	ENSNLEG00000005945	1 retrocopy	retro_nleu_1509,
Pongo abelii	ENSPPYG00000003041	1 retrocopy	retro_pabe_2471,
Pan troglodytes	ENSPTRG00000003901	1 retrocopy	retro_ptro_2016 ,