RetrogeneDB ID: retro_rnor_604

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:131469609..131469873(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufa6
• Ensembl ID: ENSRNOG00000008569
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001123977]

Sequence

>retro_rnor_604
GCTAAAGATGCAGCCCCATCATTGAAGTCCGTTTTCAGTTGTGACCTGAGTGAGGGCAACTAGAGGGTATGCAAGCTGTA
CAGCCCTTGGCATCAGGAGCTGCCATATACTGTGTACTTATTCCAGGTGGATAGCACTGTGAACCAGGAACTGAAAGAAA
TCTGAGAAACATTCATGAAGAACGCTCATGTCACAGACCCCAGAGTGTTTGATTTCCTGGTCATTAATAGAAAGATTGAG
TTCTAGGAAACCATTAAAATGTGG

Alignment

ORF - retro_rnor_604 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.55 %
• Parental protein coverage: 67.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASAASTSVKPIFSRDLKEAKRRVRELYRAWYREVPNTVHLMQLDITVKQGRDKVREMFMKNAHVTDPRVV
          A..A..S.K..FS.DL.E...RV..LY..W..E.P.TV.L.Q.D.TV.Q......E.FMKNAHVTDPRV.
Retrocopy AKDAAPSLKSVFSCDLSEGN*RVCKLYSPWHQELPYTVYLFQVDSTVNQELKEI*ETFMKNAHVTDPRVF

Parental  DLLVIKGKMELQETIKVW
          D.LVI..K.E..ETIK.W
Retrocopy DFLVINRKIEF*ETIKMW

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	32.35 RPM
SRP017611_kidney	0.00 RPM	69.71 RPM
SRP017611_liver	0.00 RPM	55.40 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_604 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_604 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_604 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona savignyi	ENSCSAVG00000001466	1 retrocopy	retro_csav_29,
Erinaceus europaeus	ENSEEUG00000004117	1 retrocopy	retro_eeur_664,
Monodelphis domestica	ENSMODG00000007030	1 retrocopy	retro_mdom_397,
Mus musculus	ENSMUSG00000022450	1 retrocopy	retro_mmus_2693,
Oryctolagus cuniculus	ENSOCUG00000015446	1 retrocopy	retro_ocun_1128,
Otolemur garnettii	ENSOGAG00000014762	2 retrocopies	retro_ogar_1656, retro_ogar_312,
Procavia capensis	ENSPCAG00000004570	1 retrocopy	retro_pcap_18,
Rattus norvegicus	ENSRNOG00000008569	1 retrocopy	retro_rnor_604 ,
Sorex araneus	ENSSARG00000003814	1 retrocopy	retro_sara_75,