RetrogeneDB ID: retro_rnor_151

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 7:123206850..123207306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000005572
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Ndufb11
• Ensembl ID: ENSRNOG00000008329
• Aliases: Ndufb11, RGD1563698
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001100226]

Sequence

>retro_rnor_151
ATGGCGGCCTGGCGGTTAAGTTTGTGCGCTCGCAGTCTTTTCGCGATTCGAGGGCTGCAGGCTGCCCCACTTCGCTGGAA
ATCCAGCTCCTCCAGGGCTGTTATCGCCCGGTCCGCTGCGGCCAGTAAGAAGCGGCGGGAAGAACCGACCATACAGTGGA
TGGAGGACCCAGAGCCCGAGGATGAAAACGTGTACTTGAAGAACCCAAACTTCCACGGTTACGACGACGACCCCAACATG
GATGTCTGGAATATGCAGGCCGTCTTCTTCTTTGGTTTTTCCATCGCCCTGGTCCTTGGCACTACCTTTGTGGCTTATGT
GCCCGACTACAGGATGCTCGAGTGGGCCCACCGGGAAGCTATGATGCTGGTGAAATACCGAGAAGCCAATGGGCTCCCCC
TCATGGAATCCAACCGGTTTGACCCCAGCAAGATCAACCTGCTGGACAATAAGTGA

Alignment

ORF - retro_rnor_151 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.0 %
• Parental protein coverage: 97.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAARLLSLYARRLSVAAAIREVPAARVRWESS--RAVIAPSGV-ERKRQREPTMVWQEDPEPEDENLYAK
          MAA..LSL.AR.L....AIR...AA..RW.SS..RAVIA.S.....KR..EPT..W.EDPEPEDEN.Y.K
Retrocopy MAAWRLSLCARSLF---AIRGLQAAPLRWKSSSSRAVIARSAAASKKRREEPTIQWMEDPEPEDENVYLK

Parental  NPDFHGYDSDPVVDVWNMRAVFFFGFSIVLVFGTTFVAYLPDYRMQEWARREAERLVKYRELNGLPIMES
          NP.FHGYD.DP..DVWNM.AVFFFGFSI.LV.GTTFVAY.PDYRM.EWA.REA..LVKYRE.NGLP.MES
Retrocopy NPNFHGYDDDPNMDVWNMQAVFFFGFSIALVLGTTFVAYVPDYRMLEWAHREAMMLVKYREANGLPLMES

Parental  NYFDPSKIQL
          N.FDPSKI.L
Retrocopy NRFDPSKINL

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	0.14 RPM	31.42 RPM
SRP017611_kidney	0.14 RPM	72.36 RPM
SRP017611_liver	0.00 RPM	34.29 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_151 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_151 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_151 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_245

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000147123	1 retrocopy	retro_hsap_912,
Macaca mulatta	ENSMMUG00000017422	2 retrocopies	retro_mmul_1116, retro_mmul_830,
Monodelphis domestica	ENSMODG00000018491	1 retrocopy	retro_mdom_1063,
Mus musculus	ENSMUSG00000031059	2 retrocopies	retro_mmus_245, retro_mmus_2602,
Pongo abelii	ENSPPYG00000020284	1 retrocopy	retro_pabe_788,
Pan troglodytes	ENSPTRG00000021836	1 retrocopy	retro_ptro_633,
Rattus norvegicus	ENSRNOG00000008329	1 retrocopy	retro_rnor_151 ,
Ictidomys tridecemlineatus	ENSSTOG00000026821	1 retrocopy	retro_itri_1084,