RetrogeneDB ID: retro_rnor_78

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 16:61538078..61538651(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000050067
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: RPS9
• Ensembl ID: ENSRNOG00000049813
• Aliases: None
• Description: None

Sequence

>retro_rnor_78
ATGCCGGTCGCCAGAAGCTGGGTTTGTCGCAAAACCTATGTGACCCCACGGAGACCCTTCGAGAAATCGCGTCTCGACCA
GGAGCTAAAGTTGATTGGAGAGTATGGACTCCGGAACAAACGTGAGGTGTGGAGGGTCAAATTTACCCTGGCGAAGATTC
GTAAGCTGTTGACGCTGGACGAGAAGGATCCTAGGTGTCTGTTTGAAGGCAACGCTCTGCTGAACCGACTTGTTCAGATT
GGGGTGCTGGATGAGGGCAAGATGAAGCTGGATTTCATTCTGGGCCTGAAGATTGAGGATTTCTTGGAGAGAAGGCTGCA
AACCCAGGTCTTTAAGCTGGGCCTGGCCAAATCTATTCACCATGCCCGTGTGCTCATCCGCCAACGTCACATCAGGGTTC
TCAAGCAGGTGGTGAACATCCCATCTTTCATTGTTCGCCTGGACTCTCAGAAGCACATTGACTTTTCCCTCCGTTCTCCT
TATGGTGGTGGCCGCCCAGGCAGAGTGAAGAGGAAGAATGCCAAGAAAGGCCAGGGTGGTGCTGGAGCTGGTGATGATGA
GGAAGAGGATTAA

Alignment

ORF - retro_rnor_78 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.36 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRKAARELLTLDEKDPRR
          MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRK....LLTLDEKDPR.
Retrocopy MPVARSWVCRKTYVTPRRPFEKSRLDQELKLIGEYGLRNKREVWRVKFTLAKIRK----LLTLDEKDPRC

Parental  LFEGNALLRRLVRIGVLDEGKMKLDYILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVRKQ
          LFEGNALL.RLV.IGVLDEGKMKLD.ILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRV.KQ
Retrocopy LFEGNALLNRLVQIGVLDEGKMKLDFILGLKIEDFLERRLQTQVFKLGLAKSIHHARVLIRQRHIRVLKQ

Parental  VVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
          VVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED
Retrocopy VVNIPSFIVRLDSQKHIDFSLRSPYGGGRPGRVKRKNAKKGQGGAGAGDDEEED

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	0.22 RPM	0.00 RPM
SRP017611_kidney	3.14 RPM	0.00 RPM
SRP017611_liver	5.51 RPM	0.00 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_78 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_78 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_78 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 ,