RetrogeneDB ID: retro_pabe_1887

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 22:36318826..36319404(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSPPYG00000010377
• Aliases: None
• Description: ribosomal protein S9 [Source:HGNC Symbol;Acc:10442]

Sequence

>retro_pabe_1887
ATGCCAGTGGCCCGGAGCTGGGTTTGTCGCAAAACTTATGTGACCCCGCGGAGACCCTTCGAGAAATCTCGTCTCGACCA
AGAGCTGAAGCTGATTGGAGAGTATGGGCTCCGGAACAAACGTGAGGTCTGGTGAGTCAAATTTACCCTGGCCAAGATCC
GCAAGGCCGCCCGGGAACTGCTGACGCTTGAAGAGAAGGACCCACGGCGTCTGTTGGAAGGCAATGCCCTGCTGCGGCGG
CTGGTCCGCAGTGGGGTGCTGGATGAGGGCAAGATGAAGCTGGATTACATCCTGGGCCTGAAGATAGAGGATTTCTTAGA
GAGACGCCTACAGACCCAGGTCTTCAAGCTGGGCTTGGCCAAGTCCACCACGCTCGCGTGCTGATCCGCCAACGCCATAT
CAGGGTCCGCAAGCAGGTGGTGAACATCCCGTCCTTCATTGTCCGCCTCGATTCCCAGAAGCACATCGACTTCTCTCTGC
GCTCTCCCTATGAGGGTGGCCGCCCGGGCCGCCTGAAGAGGAAGAATGCCAAGAAGGGCCAGGGTGGGGCTGGGGCTGGA
GACCACGAGGAGGAGGAT

Alignment

ORF - retro_pabe_1887 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.85 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR
          MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVW.VKFTLAKIRKAARELLTL.EKDPRR
Retrocopy MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVW*VKFTLAKIRKAARELLTLEEKDPRR

Parental  LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKL-GLAKSIHHARVLIRQRHIRVRK
          L.EGNALLRRLVR.GVLDEGKMKLDYILGLKIEDFLERRLQTQVFKL.GL....HHARVLIRQRHIRVRK
Retrocopy LLEGNALLRRLVRSGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKL<GLGQ-VHHARVLIRQRHIRVRK

Parental  QVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
          QVVNIPSFIVRLDSQKHIDFSLRSPY.GGRPGR.KRKNAKKGQGGAGAGD.EEED
Retrocopy QVVNIPSFIVRLDSQKHIDFSLRSPYEGGRPGRLKRKNAKKGQGGAGAGDHEEED

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	0.00 RPM	155.37 RPM
SRP007412_cerebellum	0.12 RPM	63.96 RPM
SRP007412_heart	0.09 RPM	134.53 RPM
SRP007412_kidney	0.23 RPM	412.68 RPM
SRP007412_liver	0.18 RPM	293.68 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1887 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1887 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1887 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_57
Gorilla gorilla	retro_ggor_160

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000022552	2 retrocopies	retro_mmul_1664, retro_mmul_2027,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Nomascus leucogenys	ENSNLEG00000006314	1 retrocopy	retro_nleu_91,
Pongo abelii	ENSPPYG00000010377	5 retrocopies	retro_pabe_1343, retro_pabe_1701, retro_pabe_1845, retro_pabe_1887 , retro_pabe_2671,
Rattus norvegicus	ENSRNOG00000011355	7 retrocopies	retro_rnor_1298, retro_rnor_2577, retro_rnor_2849, retro_rnor_2902, retro_rnor_635, retro_rnor_663, retro_rnor_892,
Rattus norvegicus	ENSRNOG00000049813	3 retrocopies	retro_rnor_2082, retro_rnor_30, retro_rnor_78,