RetrogeneDB ID: retro_rnor_635

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:225785120..225785696(-)
• Located in intron of: ENSRNOG00000015911

Retrocopy information

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

Parental gene information

• Parental gene symbol: Rps9
• Ensembl ID: ENSRNOG00000011355
• Aliases: None
• Description: 40S ribosomal protein S9 [Source:UniProtKB/Swiss-Prot;Acc:P29314]

Sequence

>retro_rnor_635
GTCACCAGAAGTTGGGTTTGTCGCAAAACCTATGTGACCCCACAGAGACCCTTTGAGAAATCACGTCTTGACCAGGAGCT
AAAGTTGATTGGAGAGTATGGACTCCAGAACAGACGTGAGGTGTGGAGGGTCAAATTTACCCTGGTGAAGATCCATAAGG
CTGCCTGGGAGCTATTGACACAGAACGAGAAGGATCCTGGGTGTCTGTTTGAAGTCAACGCTCTACCGAGATGACTCGTT
CAGGTTGGGGTGCTGGATGAGGGCAAGATGAAGCTGGATTACATCCTGGGCCTGAAGATTGAGGATTTCTTGGAGAGACA
GCTGCAGACCCAGGTCTTTGAGCTGGGCCTGGACCAATCTGTTCACCATGCCCGTGTGCTCATCTGCCAACGTCACGTCA
GGGTCCACAAGCAGGTGGTGAACAGCCCATCCTTCATGGTTTGCTTGGACTCCCAGAAGCACATTGACTTCTCCCTCCGT
TCTCCTTATGGTGGTGGCTGTCCAGGCTGAGTGAAGAGGAAGAATACCAAGAAAGGCCAGGGTGGTGCTGGAGCTGATGA
TGATGAGGAAGAGGAT

Alignment

ORF - retro_rnor_635 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.85 %
• Parental protein coverage: 98.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRRLF
          V.RSWVCRKTYVTP.RPFEKSRLDQELKLIGEYGL.N.REVWRVKFTL.KI.KAA.ELLT..EKDP..LF
Retrocopy VTRSWVCRKTYVTPQRPFEKSRLDQELKLIGEYGLQNRREVWRVKFTLVKIHKAAWELLTQNEKDPGCLF

Parental  EGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQVV
          E.NAL.R.LV..GVLDEGKMKLDYILGLKIEDFLER.LQTQVF.LGL..S.HHARVLI.QRH.RV.KQVV
Retrocopy EVNALPR*LVQVGVLDEGKMKLDYILGLKIEDFLERQLQTQVFELGLDQSVHHARVLICQRHVRVHKQVV

Parental  NIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
          N.PSF.V.LDSQKHIDFSLRSPYGGG.PG.VKRKN.KKGQGGAGA.DDEEED
Retrocopy NSPSFMVCLDSQKHIDFSLRSPYGGGCPG*VKRKNTKKGQGGAGADDDEEED

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
SRP017611_brain	0.00 RPM	9.56 RPM
SRP017611_kidney	0.14 RPM	14.58 RPM
SRP017611_liver	0.07 RPM	10.35 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_635 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_635 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001130	3 retrocopies	retro_cjac_2034, retro_cjac_2993, retro_cjac_719,
Cavia porcellus	ENSCPOG00000020893	2 retrocopies	retro_cpor_1457, retro_cpor_407,
Gorilla gorilla	ENSGGOG00000027839	4 retrocopies	retro_ggor_1491, retro_ggor_160, retro_ggor_2190, retro_ggor_32,
Macaca mulatta	ENSMMUG00000022552	2 retrocopies	retro_mmul_1664, retro_mmul_2027,
Mustela putorius furo	ENSMPUG00000010394	1 retrocopy	retro_mputfur_128,
Mus musculus	ENSMUSG00000006333	2 retrocopies	retro_mmus_3082, retro_mmus_526,
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,
Pan troglodytes	ENSPTRG00000011449	1 retrocopy	retro_ptro_57,
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,