RetrogeneDB ID: retro_rnor_540

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 1:248564054..248564404(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000023901
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufa11
• Ensembl ID: ENSRNOG00000048320
• Aliases: None
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 11 [Source:UniProtKB/Swiss-Prot;Acc:Q80W89]

Sequence

>retro_rnor_540
GACGGCACCCAGTGTCATCGCAAGGCCTACATCACTACTGCCTTAGGCAGCCTTTGCGGCCTAATAAGCTCTGCTTACAG
CATCACACACAACCCCGCAGATTCTCCCCTGGAAGCCGTGGCCAGGTCGGCCGGTCCACATTCACTGCAGCTGCTATCGG
AGCTATGTTTGGCCTTACCACCTGTGTCAGTGCCCAGGTCCGAGAGAAGCCAGATGAACCCTTGAACTACTTCACTGGAG
GTTGCGCAGGAGGCCTGATATTGGGAGCACGCACTCACAGCTATGGGACCGCCGCCATTGGCTGTGTCTATAAGCTGGAG
GGCTGGGAACTGTTTGCCACCCCCAAGGTG

Alignment

ORF - retro_rnor_540 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.44 %
• Parental protein coverage: 82.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DGTQCHRKAYITTALGGLCGLISSAYSITHNPADSPLEAVAR-VGRFTFTAAAIGAMFGLTTCVSAQVRE
          DGTQCHRKAYITTALG.LCGLISSAYSITHNPADSPLEAVAR.VGR.TFTAAAIGAMFGLTTCVSAQVRE
Retrocopy DGTQCHRKAYITTALGSLCGLISSAYSITHNPADSPLEAVAR<VGRSTFTAAAIGAMFGLTTCVSAQVRE

Parental  KPDDPLNYFIGGCAGGLTLGARTHSYGTAAIGCVYMGTAAALFKMGKL
          KPD.PLNYF.GGCAGGL.LGARTHSYGTAAIGCVY......LF...K.
Retrocopy KPDEPLNYFTGGCAGGLILGARTHSYGTAAIGCVYKLEGWELFATPKV

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	27.97 RPM
SRP017611_kidney	0.00 RPM	63.57 RPM
SRP017611_liver	0.00 RPM	45.79 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_540 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_540 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_540 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000002379	1 retrocopy	retro_mmus_1450,
Rattus norvegicus	ENSRNOG00000048320	1 retrocopy	retro_rnor_540 ,