RetrogeneDB ID: retro_pabe_1343

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 16:11958831..11959400(+)
• 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_1343
CGGAGCTGGGTTTGTCGCAAACTGTATGTGACCCCGCGGAGACCCTTCTTAGAAATCTCGTCTCGACCAAGAGCTGAAGC
TGATCGGCGGGTATGGGCTCCGGAACAAACGTGAGGTCTGGAGCGTCAAATTTACCCTGGCCAAGATCCACAAGGCCGCC
CGGGAACTGCTGACGCTTGATGAGAAGGACCCACGGCGTCTGTTCGAAGGCAACGCCCTGCTGCGGCGGCTGGTCCGCAT
TGGGGTGCTGGATGAGGGCAAGATGAAGCTGGATTACCATCCTGGGCCTGAAGATAGAGGATTTCTTAGAGAGACGCCTT
CAGACCCAGGTGTTCCAGGCTGGGCTTGGCCAAGTCCATCCCACCACGCTCGCGTGCTGATCCCGCCAGCGCCCTATCAG
GGTCCGCAAGCAGGTGGTGAACATCCCGTCCTTCATTGTCCGCCTGGATTCCCAGAAGCACATCGACTTCTCTCTGCGCT
CTCCCTGTGGGGGTGGCCGCCCGGGCCGCGTGAAGAGGAAGAACGCCAAGAAGGGCCAGCGTGGGGCCGGGGCTGGAGAC
GACGAGGAG

Alignment

ORF - retro_pabe_1343 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.75 %
• Parental protein coverage: 96.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RSWVCRKTYVTPRRPFE-KSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLFE
          RSWVCRK.YVTPRRPF..KSRLDQELKLIG.YGLRNKREVW.VKFTLAKI.KAARELLTLDEKDPRRLFE
Retrocopy RSWVCRKLYVTPRRPFL>KSRLDQELKLIGGYGLRNKREVWSVKFTLAKIHKAARELLTLDEKDPRRLFE

Parental  GNALLRRLVRIGVLDEGKMKLDY-ILGLKIEDFLERRLQTQVF-KLGLAKSI-HHARVLI-RQRHIRVRK
          GNALLRRLVRIGVLDEGKMKLDY.ILGLKIEDFLERRLQTQVF..LGLAKSI.HHARVLI.RQR.IRVRK
Retrocopy GNALLRRLVRIGVLDEGKMKLDY>ILGLKIEDFLERRLQTQVF>RLGLAKSI>HHARVLI>RQRPIRVRK

Parental  QVVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEE
          QVVNIPSFIVRLDSQKHIDFSLRSP.GGGRPGRVKRKNAKKGQ.GAGAGDDEE
Retrocopy QVVNIPSFIVRLDSQKHIDFSLRSPCGGGRPGRVKRKNAKKGQRGAGAGDDEE

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	0.11 RPM	155.37 RPM
SRP007412_cerebellum	0.00 RPM	63.96 RPM
SRP007412_heart	0.06 RPM	134.53 RPM
SRP007412_kidney	0.30 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_1343 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1343 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1343 has 0 orthologous retrocopies within eutheria group .

---

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,