RetrogeneDB ID: retro_pabe_3051

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:22924816..22925751(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IGLON5
• Ensembl ID: ENSPPYG00000010315
• Aliases: None
• Description: IgLON family member 5 [Source:HGNC Symbol;Acc:34550]

Sequence

>retro_pabe_3051
AGCCGAGGGCTGCTCTCCCAGAGCCTGGAGTTCAACTCTCCTGCCGACAACTACACAGTGTGTGAAGGTGACAACGCCAC
CCTCAGCTGCTTCATCGACGAGCATGTGACCTGCGTGGCCTGGCTGAACTGCTCCAACATCCTGTACGCCGGCAACGACC
ACAGGACCAGAGACCCGCGGGTGCGGCTGCTCATCAACACCCCCGAGGAGTTCTCCATCCTCATCACCGAGGTGGGGCTC
GGCGACGAGGGCCTCTACACCGGCTCCTTCCAGACCCGCCACCAGCCGTACACCACTCAGGTCTACCTCATTGTCCACGT
CCCTGCCCGCATTGTGACATCTCGTCGCCTGTGATGGTGAATGAGGGGGGTAATGTGAACCTGCTTTGCCTGGCCGTGGG
GCGGCCAGAGCCCACGGTCACCTGGAGACAGCTGCGAGACGGCTTCACCTCGGAGGGAGAGATCCTGGAGATCTCTGACA
TCCAGCGGGGCCAGGCCGGGGAGTATGAGTGCGTGACTCACAACGGGGTTAACTAGGCGCCCGACAGCCGCCGCGTGCTG
GTCACAGTCAACTATCCTCCGACCATCAGGGACGTGACCAGCGCCCGCACTGCGCTGGGCCGGGCCGCCCTCCTGCGCTG
CGAAGCTATGGCGGTTCCCCCCGCGGATTTCCAGTGGTACAAGGATGACAGACTGCTGAGCAGCGGCACGGCCGAGGGCC
TGAAGGTGCAGAGGGAGCGCACCCGCTCGATGCTTCTCTTTGCCAACATGAGCGCCCGGCATTTCGGCAACTATACCTGT
CGCGCCGCCAACCGGATGGGAGCGTCCAGCGCCTCCATCCGGCTCCTGCGCCCAGGATCCCTGGAGAACTCAGCCCCGAG
GCCCCCAGGGCCCCTGGCCCTCCTCTCCGCCCTGGGTTGGCTGTGGTGGAGAATG

Alignment

ORF - retro_pabe_3051 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.57 %
• Parental protein coverage: 97.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  STGLLSQSLEFNSPADNYTVCEGDNATLSCFIDEHVTRVAWLNRSNILYAGNDRWTSDPRVRLLINTPEE
          S.GLLSQSLEFNSPADNYTVCEGDNATLSCFIDEHVT.VAWLN.SNILYAGND..T.DPRVRLLINTPEE
Retrocopy SRGLLSQSLEFNSPADNYTVCEGDNATLSCFIDEHVTCVAWLNCSNILYAGNDHRTRDPRVRLLINTPEE

Parental  FSILITEVGLGDEGLYTCSFQTRHQPYTTQVYLIVHVPARIV-NISSPVTVNEGGNVNLLCLAVGRPEPT
          FSILITEVGLGDEGLYT.SFQTRHQPYTTQVYLIVHVPARIV..ISSPV.VNEGGNVNLLCLAVGRPEPT
Retrocopy FSILITEVGLGDEGLYTGSFQTRHQPYTTQVYLIVHVPARIV<DISSPVMVNEGGNVNLLCLAVGRPEPT

Parental  VTWRQLRDGFTSEGEILEISDIQRGQAGEYECVTHNGVNSAPDSRRVLVTVNYPPTITDVTSARTALGRA
          VTWRQLRDGFTSEGEILEISDIQRGQAGEYECVTHNGVN.APDSRRVLVTVNYPPTI.DVTSARTALGRA
Retrocopy VTWRQLRDGFTSEGEILEISDIQRGQAGEYECVTHNGVN*APDSRRVLVTVNYPPTIRDVTSARTALGRA

Parental  ALLRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQTERTRSMLLFANVSARHYGNYTCRAANRLGASSAS
          ALLRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQ.ERTRSMLLFAN.SARH.GNYTCRAANR.GASSAS
Retrocopy ALLRCEAMAVPPADFQWYKDDRLLSSGTAEGLKVQRERTRSMLLFANMSARHFGNYTCRAANRMGASSAS

Parental  MRLLRPGSLENSAPRPPGPLALLSALGWLWWRM
          .RLLRPGSLENSAPRPPGPLALLSALGWLWWRM
Retrocopy IRLLRPGSLENSAPRPPGPLALLSALGWLWWRM

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	0.61 RPM	25.43 RPM
SRP007412_cerebellum	0.73 RPM	52.90 RPM
SRP007412_heart	0.00 RPM	0.09 RPM
SRP007412_kidney	0.00 RPM	0.99 RPM
SRP007412_liver	0.00 RPM	0.06 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3051 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3051 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3051 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2628

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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,