RetrogeneDB ID: retro_rnor_2374

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 6:72382862..72383927(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000045967
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufa10
• Ensembl ID: ENSRNOG00000016470
• Aliases: Ndufa10, ndufa10l
• Description: NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:Q561S0]

Sequence

>retro_rnor_2374
ATGGCCTTGAGGTTGCTGAGACTTGTCCCGGCGTCGGCGTCCGCGCGCGGCCTCGCGGCCGGAGCCCAGCGCGTGGGACG
AATTCATACCAGTGTGCACTGCAAGCTGAGGTACGGGCTTTTGGCTTCCATTCTCGGTGATAAGACAACCAAAAAGCTGC
ATGAGTACAGCCGAGTGATAACAGTAGATGGCAACATATGCTCTGGGAAAAACAAGCTCGCAAGGGACATCGCAGAGCAG
CTAGGCATGAAGCACTATCCGGAAGCAGGGATACAGTACTCAAGCAGCACCACGGGTGACGGAAGGCCCCTCGACATAGA
GTTTAGTGGCAGCTGTAGTTTAGAGAAATTTTATGACGATCCCAAAAGCAACGACGGCAACAGCTACCGCCTACAGTCCT
GGCTTTATGCCAGCCGCCTCCTGCAGTACTCAGACGCCCTGGAGCACCTCTTGAGCACAGGACAAGGTGTGGTCTTGGAG
CGTTCCATCTACAGTGACTTTGTCTTCCTGGAGGCAATGTACAACCGGGGCTTCATCCGAAAGCAGTGTGTGGACCACTA
TAATGAAATTAAGCGGCTTACTCTTCCAGAGTACCTGCCATCACATGCAGTCATCTATATCGATGTGCCTGTGTCAGAAA
TACAGAGCAGGATCCAGAAGAAAGGAGATCCACATGAAATGAAGGTCACCTCTGCCTATCTCCAGGACATCGAGGATGCC
TACAAGAAAACCTTCCTCCCACAAATGAGTGAGATATGCGAGGTGTTGATGTACAGTTCCTGGGAAGCTGAAGACTCAAC
CAAGGTGGTAGAGGACATTGAGTACCTTAACTACAACAAAGGACCTTGGCTTAAACAGGATGATCGGACCTTTCACAACC
TGCGAATGCTGGTCCAGGATAAGAGAGAAGTGCTGAATTACACGACTGTCCCGGTTTACCTCCCAGAAATCACTATTGGA
GCTCATCAGGGTAGCCGGATCTACGACAGCTTCAGAGAGCTGCCAGGCCGCAAGTACGCCCCTGGGTACAATGCCGATGT
GGGTGACAAGTGGATCTGGCTGAAG

Alignment

ORF - retro_rnor_2374 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.59 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALRLLRLVPASASARGLAAGAQRVGRIHTSVHCKLRYGLLASILGDKTTKKLHEYSRVITVDGNICSGK
          MALRLLRLVPASASARGLAAGAQRVGRIHTSVHCKLRYGLLASILGDKTTKKLHEYSRVITVDGNICSGK
Retrocopy MALRLLRLVPASASARGLAAGAQRVGRIHTSVHCKLRYGLLASILGDKTTKKLHEYSRVITVDGNICSGK

Parental  NKLARDIAEQLGMKHYPEAGIQYSSSTTGDGRPLDIEFSGSCSLEKFYDNPKSNDGNSYRLQSWLYASRL
          NKLARDIAEQLGMKHYPEAGIQYSSSTTGDGRPLDIEFSGSCSLEKFYD.PKSNDGNSYRLQSWLYASRL
Retrocopy NKLARDIAEQLGMKHYPEAGIQYSSSTTGDGRPLDIEFSGSCSLEKFYDDPKSNDGNSYRLQSWLYASRL

Parental  LQYSDALEHLLSTGQGVVLERSIYSDFVFLEAMYNQGFIRKQCVDHYNEIKRLTLPEYLPPHAVIYIDVP
          LQYSDALEHLLSTGQGVVLERSIYSDFVFLEAMYN.GFIRKQCVDHYNEIKRLTLPEYLP.HAVIYIDVP
Retrocopy LQYSDALEHLLSTGQGVVLERSIYSDFVFLEAMYNRGFIRKQCVDHYNEIKRLTLPEYLPSHAVIYIDVP

Parental  VSEIQSRIQKKGDPHEMKVTSAYLQDIEDAYKKTFLPKMSEICEVLVYSSWEAEDSTKVVEDIEYLNYNK
          VSEIQSRIQKKGDPHEMKVTSAYLQDIEDAYKKTFLP.MSEICEVL.YSSWEAEDSTKVVEDIEYLNYNK
Retrocopy VSEIQSRIQKKGDPHEMKVTSAYLQDIEDAYKKTFLPQMSEICEVLMYSSWEAEDSTKVVEDIEYLNYNK

Parental  GPWLKQDDRTFHNLRMLVQDKREVLNYTTVPVYLPEITIGAHQGSRIYDSFRELPGRKYAPGYNADVGDK
          GPWLKQDDRTFHNLRMLVQDKREVLNYTTVPVYLPEITIGAHQGSRIYDSFRELPGRKYAPGYNADVGDK
Retrocopy GPWLKQDDRTFHNLRMLVQDKREVLNYTTVPVYLPEITIGAHQGSRIYDSFRELPGRKYAPGYNADVGDK

Parental  WIWLK
          WIWLK
Retrocopy WIWLK

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	1.08 RPM	61.26 RPM
SRP017611_kidney	0.35 RPM	103.84 RPM
SRP017611_liver	0.54 RPM	48.61 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_rnor_2374 retrocopy.

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_2374 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_2374 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Rattus norvegicus	ENSRNOG00000016470	1 retrocopy	retro_rnor_2374 ,