RetrogeneDB ID: retro_pabe_2471

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 4:133032863..133033676(+)
• Located in intron of: ENSPPYG00000029828

Retrocopy information

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

Parental gene information

• Parental gene symbol: FOSL1
• Ensembl ID: ENSPPYG00000003041
• Aliases: None
• Description: FOS-like antigen 1 [Source:HGNC Symbol;Acc:13718]

Sequence

>retro_pabe_2471
ATGTTCTGAGACTTCAGGGAACCCGGCCCGAGCTCCGGGAATGGGGCGGGTATGGCGGCCCCGCGCAGCCCCCCGGCTGC
AGCGCAGGCAGCCCAGCAGAAATTCCACCTCGTGCCAAGGATCAACAACATGAGTGGCAGTCAGGAGCTGCAGTGGATGG
TACAGCCTCATTTTCTGGGGCCCAGCAGTTACCCCAGGCCTCTGACCTACCCTTAGTCCAGCCCTCCACAACCCCAGCCA
GGAGTCATCCGGGCCCTGGGGCCGCCTCCAGGGGTGTGTCCAAGGCCTTGTGAACAGATCAGCCCGCAGGAAGAGGAGCG
CCGCCGAGTAAGGCCCGAGCGGAACAAGCTGGCTGCGGCCAAGTGTAGGAACTGGAGGAAGGAACTGACTGACTTCCTGC
AGGCGGAGACTGATAAACTGGAAGATGAGAAATCCGGGCTGCAGCGAGAGATTGAGGAGCTGCAGAAGCAGATGGAGCGC
CTGGAGCTGGTGCTGGAAGCCCACTGACCCACCTGCACAATCCCCGAAGGAGCCAAGGAGGGGGACACAGGCGGTACCAG
CGGCACCAGCAGCCCGCCAGCCCCCTGCCGCCCTGTACCTGGTATCTCCCTTTCCCCAGGGCCTGTGCTTGAACCTGAGG
CACTGCACACCCCCAAGCTCATGACCACACCCTCCCTGACTCCTTTCACCCCCAGCCTGGTCTTCACCTACCCCAGCACT
CCTGAGCCCTGTGCCTCAGCTCATCACAAGAGTAGCAGCAGCAGCGGAGACCCATCCTCTGACCCCCTTGGCTCTCCAAC
CCTCCTCGCTTTG

Alignment

ORF - retro_pabe_2471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.58 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MFRDFGEPGPSSGNG-GGYGGPAQPP-AAAQAAQQKFHLVPSINTMSGSQELQWMVQPHFLGPSSYPRPL
          MF.DF.EPGPSSGNG.GGYGGPAQPP.AAAQAAQQKFHLVP.IN.MSGSQELQWMVQPHFLGPSSYPRPL
Retrocopy MF*DFREPGPSSGNG<GGYGGPAQPP>AAAQAAQQKFHLVPRINNMSGSQELQWMVQPHFLGPSSYPRPL

Parental  TYPQYSPPQPRPGVIRALGPPPGVRRRPCEQISP-EEERRRVRRERNKLAAAKCRNRRKELTDFLQAETD
          TYP..SPPQP.PGVIRALGPPPGV..RPCEQISP.EEERRRVR.ERNKLAAAKCRN.RKELTDFLQAETD
Retrocopy TYP*SSPPQPQPGVIRALGPPPGVCPRPCEQISPQEEERRRVRPERNKLAAAKCRNWRKELTDFLQAETD

Parental  KLEDEKSGLQREIEELQKQKERLELVLEAHRPICKIPEGAKDGDTGSTSGTSSPPAPCRPVPCISLSPGP
          KLEDEKSGLQREIEELQKQ.ERLELVLEAH.P.C.IPEGAK.GDTG.TSGTSSPPAPCRPVP.ISLSPGP
Retrocopy KLEDEKSGLQREIEELQKQMERLELVLEAH*PTCTIPEGAKEGDTGGTSGTSSPPAPCRPVPGISLSPGP

Parental  VLEPEALHTPTLMTTPSLTPFTPSLVFTYPSTPEPCASAHRKSSSSSGDPSSDPLGSPTLLAL
          VLEPEALHTP.LMTTPSLTPFTPSLVFTYPSTPEPCASAH.KSSSSSGDPSSDPLGSPTLLAL
Retrocopy VLEPEALHTPKLMTTPSLTPFTPSLVFTYPSTPEPCASAHHKSSSSSGDPSSDPLGSPTLLAL

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	0.17 RPM
SRP007412_cerebellum	0.00 RPM	0.12 RPM
SRP007412_heart	0.00 RPM	0.87 RPM
SRP007412_kidney	0.10 RPM	0.33 RPM
SRP007412_liver	0.12 RPM	2.05 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2471 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2471 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2471 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2981
Pan troglodytes	retro_ptro_2016
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,