RetrogeneDB ID: retro_rnor_1491

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 2:47002448..47002786(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ndufa7
• Ensembl ID: ENSRNOG00000006939
• Aliases: None
• Description: NADH dehydrogenase [Source:RefSeq peptide;Acc:NP_001100242]

Sequence

>retro_rnor_1491
ATGGTGTCTGCTACTTGCGCTATACAAAAGCTGTGGAACTGAGCGTCTGAGCAAGATCTGCAGGTGAAGCTGCAGCTGCA
CTACCAGGAGATCCCCGAGCCGACCCAGCCACCTCCAAAGCGCCCCGTAGGCCCCAGTCACAAGCTGTCCAACAGTTACT
ACTGTGCTCGTGATGGCAGCTGGGAAGTTGTGCCTCCCTCAGTCATCATGTCCTTACAAAAGGCCCTGGTGTTGGGCAAG
ACAGCTTTGAGTTCTGCTGTGGCAGCCACTGAAAAGAGGGCAGTGAACCTGCTCCTCCCATGGAGAGGTGGGAGCTGTCC
AAGGCCCAGCCATACCTG

Alignment

ORF - retro_rnor_1491 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASATRVIQKLRNWASGQDLQAKLQLRYQEIAKRTQPPPKLPVGPSHKLSNNYYCTRDGRREVVPPSIIM
          M.SAT..IQKL.N.AS.QDLQ.KLQL.YQEI...TQPPPK.PVGPSHKLSN.YYC.RDG..EVVPPS.IM
Retrocopy MVSATCAIQKLWN*ASEQDLQVKLQLHYQEIPEPTQPPPKRPVGPSHKLSNSYYCARDGSWEVVPPSVIM

Parental  SSQKALVSGKTAESSAVAAT-KRAVT-PAPPMKRWELSRDQPYL
          S.QKALV.GKTA.SSAVAAT.KRAV..PAPPM.RWELS..QPYL
Retrocopy SLQKALVLGKTALSSAVAATEKRAVN<PAPPMERWELSKAQPYL

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	20.42 RPM
SRP017611_kidney	0.00 RPM	31.05 RPM
SRP017611_liver	0.00 RPM	23.26 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_1491 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1491 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1491 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000685	1 retrocopy	retro_chof_2004,
Callithrix jacchus	ENSCJAG00000010709	2 retrocopies	retro_cjac_2942, retro_cjac_956,
Dipodomys ordii	ENSDORG00000012324	1 retrocopy	retro_dord_155,
Macropus eugenii	ENSMEUG00000015637	3 retrocopies	retro_meug_1487, retro_meug_149, retro_meug_587,
Rattus norvegicus	ENSRNOG00000006939	2 retrocopies	retro_rnor_1491 , retro_rnor_1793,