RetrogeneDB ID: retro_mmus_1450

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 16:22053503..22053932(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000068487
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufa11
• Ensembl ID: ENSMUSG00000002379
• Aliases: Ndufa11, 2010012C24Rik, AV006275, B14.7
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 11 [Source:MGI Symbol;Acc:MGI:1917125]

Sequence

>retro_mmus_1450
ATGGCGATGGCGAAGCGGTTCTTTGAATCCTACAATGAGGTCCCCGATGGTACCCAGTGTCATCGCAAGACCTACATCAC
CACTGCCTTAGGCGGCATTTGCGGCATAATCGGCTCCGCTTACAGCGTCACACTCAACCCCACAGACTCCACCCTGGAAG
CAGTGGCCAGAGTCGGCCGGTACACACTCACTGCAGCTGCTATCAGAGCGATGTTTGGCCTTACCACCTGTGTCAGTGCC
CAGGTCCGAGAGAAGCCAGATGACCCCCTGAACTACTTCATTGGCAACGGCGCAGGAGGCCTGACATTGGGAGTGCGCAC
TCACAGCTATGGGACCGCAGCCATGGGCTGTGTCTACATGGGCACTGCAGCTGCCCTGTTCAAGATCGGCAAGCTGGAAG
GCTGGGAGTTGTTCCCTACCCCCAAGGTG

Alignment

ORF - retro_mmus_1450 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.71 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAMVKRFFESYHEVPDGTQCHRKTYITTALGGICGIIGSAYSVSLNPADSTLEAVARVGRYTFTAAAIGA
          MAM.KRFFESY.EVPDGTQCHRKTYITTALGGICGIIGSAYSV.LNP.DSTLEAVARVGRYT.TAAAI.A
Retrocopy MAMAKRFFESYNEVPDGTQCHRKTYITTALGGICGIIGSAYSVTLNPTDSTLEAVARVGRYTLTAAAIRA

Parental  MFGLTTCVSAQVREKPDDPLNYFIGGCAGGLTLGARTHSYGTAAMGCVYMGTAAALFKIGKLEGWELFPT
          MFGLTTCVSAQVREKPDDPLNYFIG..AGGLTLG.RTHSYGTAAMGCVYMGTAAALFKIGKLEGWELFPT
Retrocopy MFGLTTCVSAQVREKPDDPLNYFIGNGAGGLTLGVRTHSYGTAAMGCVYMGTAAALFKIGKLEGWELFPT

Parental  PKV
          PKV
Retrocopy PKV

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
SRP007412_brain	0.05 RPM	35.09 RPM
SRP007412_cerebellum	0.00 RPM	32.09 RPM
SRP007412_heart	0.12 RPM	177.26 RPM
SRP007412_kidney	0.04 RPM	69.38 RPM
SRP007412_liver	0.00 RPM	27.12 RPM
SRP007412_testis	2.29 RPM	14.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1450 was not detected

EST

No EST(s) were mapped for retro_mmus_1450 retrocopy.

TSS

No TSS is located nearby retro_mmus_1450 retrocopy 5' end.

Lab

retro_mmus_1450 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1450 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,