RetrogeneDB ID: retro_rnor_1793

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 3:65990496..65990835(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000028492
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

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

Sequence

>retro_rnor_1793
ATGGCGTCCACTACTCGCACTATCCAAAAGCTGCTGAACTGGGCGTCTGGGCAAGACCGGCAGGCGAAGTTGCAGCTGCG
CTACCTGGAGATCACCAAGTGGACCCAGCCACCTCCGAAGCTTCCTGTGGGCCCCAGTCACAAGCTGCCCAACAATTACT
ACTGTACTCATGATGGCCGCCGGGAAGTTGTGCCTCCCTCTATCATCATGTCCTCACAAAATGCCCTAGTGTTGGGCAAG
ACAGCTGAGAGTTCTGCTGTAGCAGCCATTGAGAAGAGGGCAATGACACCTGCTCCTCCCATGGAGAGGTGGGAGCTGTC
CAGGGACCAGCCATACCTG

Alignment

ORF - retro_rnor_1793 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASATRVIQKLRNWASGQDLQAKLQLRYQEIAKRTQPPPKLPVGPSHKLSNNYYCTRDGRREVVPPSIIM
          MAS.TR.IQKL.NWASGQD.QAKLQLRY.EI.K.TQPPPKLPVGPSHKL.NNYYCT.DGRREVVPPSIIM
Retrocopy MASTTRTIQKLLNWASGQDRQAKLQLRYLEITKWTQPPPKLPVGPSHKLPNNYYCTHDGRREVVPPSIIM

Parental  SSQKALVSGKTAESSAVAA-TKRAVTPAPPMKRWELSRDQPYL
          SSQ.ALV.GKTAESSAVAA..KRA.TPAPPM.RWELSRDQPYL
Retrocopy SSQNALVLGKTAESSAVAAIEKRAMTPAPPMERWELSRDQPYL

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	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_1793 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_1793 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_1793 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 ,