RetrogeneDB ID: retro_ptro_2628

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 7:62817474..62818399(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040560
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: IGLON5
• Ensembl ID: ENSPTRG00000011377
• Aliases: None
• Description: IgLON family member 5 [Source:HGNC Symbol;Acc:34550]

Sequence

>retro_ptro_2628
CTGCTCTCCCAGAGCCTGGAGTTCAACTCTCCTGCCGACAACTATACAGTGTGTGAAGGTGACAACGCCACCCTCAGCTG
CTTCATGGACGAGCATGTGACCCGCGTGGCCTGGCTGAACCGCTCCAACATCCTGTACGCCGGCAACGACCGCAGGACCA
GCGACCCGCGGGTGCGGCTGCTCATCAACACCCCCGAAGAGTTCTCCATCCTCATCACCGAGGTGGGGCTCGGCGACGAG
GGCCTCTACACCTGCTCCTTCCAGACCCGCCACCAGCCGTACACCACTCAGGTCTACCTCATTGTCCACGTCCCTGCCTG
CGTTGTAAACATCTCGTCGCCTGTGACGGTGAATGAGGGGGGTAATGTGAACCTGCTTTGCCTGGCCGTGGGGCGGCCAG
AGCCCACGGTCACCTGGAGACAGCTCCGAGACGGCTTCACCTCGGAGGGAGAGATCCTGGAGATCTCTGACATCCAGCGG
GGCCAGGCCGGGAGTATGAGTGCGTGACTCACAACGGGGTTAACTCGGCGTCCGACAGCCGCCGCGTGCTGGTCACAGTC
AACTATCCTCCGACCATCACGGACGTGACCAGCGCCCGCACCGCGCTGGGCCGGGCCGCCTACTGCGCTGCGAAGCCATG
GCGGTTTCCCCCGCGGATTTCCAGTGGTATAAGGATGACAGACTGCTGAGCAGCGGCACGGCCGAGGGCCTGAAGGTGCA
GACGGAGCGCACCCGCTCGATGCTTCTCTTTGCCAACATGAGCGCCCGGCATTACGGCAACTATACGTGTTGCGCCGCCA
ACCGGCTGGGAGCGTCCAGCGCCTCCACGCGGCTCCTGTGCCCAGGATCCCTGGAGAACTCAGCTCTGAGGCCCCCAGGG
CCCCTGGCCCTCCTCTCCGCCCTGGGCTGGCTGTGGTGGAGAATG

Alignment

ORF - retro_ptro_2628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LLSQSLEFNSPADNYTVCEGDNATLSCFIDEHVTRVAWLNRSNILYAGNDRWTSDPRVRLLINTPEEFSI
          LLSQSLEFNSPADNYTVCEGDNATLSCF.DEHVTRVAWLNRSNILYAGNDR.TSDPRVRLLINTPEEFSI
Retrocopy LLSQSLEFNSPADNYTVCEGDNATLSCFMDEHVTRVAWLNRSNILYAGNDRRTSDPRVRLLINTPEEFSI

Parental  LITEVGLGDEGLYTCSFQTRHQPYTTQVYLIVHVPARIVNISSPVTVNEGGNVNLLCLAVGRPEPTVTWR
          LITEVGLGDEGLYTCSFQTRHQPYTTQVYLIVHVPA..VNISSPVTVNEGGNVNLLCLAVGRPEPTVTWR
Retrocopy LITEVGLGDEGLYTCSFQTRHQPYTTQVYLIVHVPACVVNISSPVTVNEGGNVNLLCLAVGRPEPTVTWR

Parental  QLRDGFTSEGEILEISDIQRGQAG-EYECVTHNGVNSAPDSRRVLVTVNYPPTITDVTSARTALGRAA-L
          QLRDGFTSEGEILEISDIQRGQAG.EYECVTHNGVNSA.DSRRVLVTVNYPPTITDVTSARTALGRAA.L
Retrocopy QLRDGFTSEGEILEISDIQRGQAG<EYECVTHNGVNSASDSRRVLVTVNYPPTITDVTSARTALGRAA<L

Parental  LRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQTERTRSMLLFANVSARHYGNYTCRAANRLGASSASMR
          LRCEAMAV.PADFQWYKDDRLLSSGTAEGLKVQTERTRSMLLFAN.SARHYGNYTC.AANRLGASSAS.R
Retrocopy LRCEAMAVSPADFQWYKDDRLLSSGTAEGLKVQTERTRSMLLFANMSARHYGNYTCCAANRLGASSASTR

Parental  LLRPGSLENSAPRPPGLLALLSALGWLWWRM
          LL.PGSLENSA.RPPG.LALLSALGWLWWRM
Retrocopy LLCPGSLENSALRPPGPLALLSALGWLWWRM

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	0.45 RPM	33.78 RPM
SRP007412_cerebellum	0.72 RPM	59.94 RPM
SRP007412_heart	0.03 RPM	0.06 RPM
SRP007412_kidney	0.05 RPM	3.30 RPM
SRP007412_liver	0.07 RPM	3.70 RPM
SRP007412_testis	0.21 RPM	8.54 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2628 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2628 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2628 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_3051

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Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000142549	1 retrocopy	retro_hsap_3857,
Gorilla gorilla	ENSGGOG00000011245	1 retrocopy	retro_ggor_2598,
Pongo abelii	ENSPPYG00000010315	1 retrocopy	retro_pabe_3051,
Pan troglodytes	ENSPTRG00000011377	1 retrocopy	retro_ptro_2628 ,