RetrogeneDB ID: retro_rnor_1056

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 14:63783072..63783461(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufb10
• Ensembl ID: ENSRNOG00000014568
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001102913]

Sequence

>retro_rnor_1056
ACCAGCCTGAGAGAGCCTTTTGAATGGCAGCATGCCAATAACTGAACTTGTTGCTATCACCAATAGTAGGGATGTGTGCA
GGACATTGCCAAATACAAGGAGGGTGATATCCTGTGTATATTCGAGGCTGGGATGCACTTAAGAAGGGACTAAAAGGTTG
ACCAGAATGTCATCCGTATCAGTCAGGAAAGGCTTAAGTCTTGTCAGCAGAAGGAAGGAGCAAACACAAGCAGATTCGTG
TCAAGGCACTGGAGCAGTTTACCAAGGTGGATAAACTCTACCACAATCGCTTTTATGACCTGGGAGCTCTTTATTTCTGC
CAGAAAGTGTCTGAGAAAGCAGAAGCAGGGGATGCTGGGAAGAGAATGGCTGCTGAGGAGACTGTTGCT

Alignment

ORF - retro_rnor_1056 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.14 %
• Parental protein coverage: 73.86 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TLVREFIEQQHAKNRTYYYHRQYRRVPDITECKEGDVICIYEAEMQWRRDFKVDQEIINIIQERLKACQQ
          T..RE..E.QHA.N.T..YH.....V.DI...KEGD..CI.EA.M..RRD.KVDQ..I.I.QERLK.CQQ
Retrocopy TSLREPFEWQHANN*TCCYHQ**GCVQDIAKYKEGDILCIFEAGMHLRRD*KVDQNVIRISQERLKSCQQ

Parental  REGESAL-QNCAKELEQFTQVSKAYQDRYQDLGAYY-SARKCLAKQKQRML-EERKAAKETAA
          .EG.....Q...K.LEQFT.V.K.Y..R..DLGA.Y.SARKCL.KQKQ.ML...R.AA.ET.A
Retrocopy KEGANTS<QIRVKALEQFTKVDKLYHNRFYDLGALY>SARKCLRKQKQGML<GKRMAAEETVA

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	52.63 RPM
SRP017611_kidney	0.00 RPM	85.13 RPM
SRP017611_liver	0.00 RPM	40.01 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1056 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1056 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1056 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Mus musculus	retro_mmus_2566

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019476	1 retrocopy	retro_cfam_1861,
Echinops telfairi	ENSETEG00000017154	1 retrocopy	retro_etel_1955,
Felis catus	ENSFCAG00000011738	1 retrocopy	retro_fcat_307,
Homo sapiens	ENSG00000140990	2 retrocopies	retro_hsap_1573, retro_hsap_3801,
Gorilla gorilla	ENSGGOG00000009367	2 retrocopies	retro_ggor_1198, retro_ggor_2555,
Latimeria chalumnae	ENSLACG00000013152	1 retrocopy	retro_lcha_100,
Macaca mulatta	ENSMMUG00000029268	1 retrocopy	retro_mmul_2218,
Mus musculus	ENSMUSG00000040048	1 retrocopy	retro_mmus_2566,
Nomascus leucogenys	ENSNLEG00000008867	1 retrocopy	retro_nleu_1740,
Pongo abelii	ENSPPYG00000006974	2 retrocopies	retro_pabe_1297, retro_pabe_3106,
Pan troglodytes	ENSPTRG00000007618	2 retrocopies	retro_ptro_1060, retro_ptro_2578,
Rattus norvegicus	ENSRNOG00000014568	1 retrocopy	retro_rnor_1056 ,
Sus scrofa	ENSSSCG00000030328	1 retrocopy	retro_sscr_689,