RetrogeneDB ID: retro_mmus_2453

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:40116818..40117172(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081352
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Ndufa13
• Ensembl ID: ENSMUSG00000036199
• Aliases: Ndufa13, 2700054G14Rik, AU022060, CDA016, CGI-39, GRIM-19, Grim19
• Description: NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 [Source:MGI Symbol;Acc:MGI:1914434]

Sequence

>retro_mmus_2453
CCTGGCTGGGGAGTGTCGGGGTGGAGCGTGTTTTCTGTGGGCATCGGGGCCTTGATCTTTGGCTACTGGAGAATGATGAG
GTGGAACCAGGAGCGCAGGAGCCTGCTGATCGAGGACTTGGAGGCCAGGATCGCCCTCATGCCGCTCTTCCAGGCAGAGA
AAGACCAGAGGACCTTGCAGATTCTTCGGGAGAATCCAGAGGAGGCCATCATTATGAAAGATGTGCCCAACTCGAAGGTG
GGCGAGTCTGTGTTCCACAGTACACGATAATTACCACCCCTCCTTGACGAGATGTATGGGTTGCGCACCAAGAAGTATAT
GAACAACGCCAGCTTCGGCTTCACCTGGTAGACT

Alignment

ORF - retro_mmus_2453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.35 %
• Parental protein coverage: 82.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PRRGLSGYSMFAVGIGALIFGYWRMMRWNQERRRLLIEDLEARIALMPLFQAEKDRRTLQILRENLEEEA
          P..G.SG.S.F.VGIGALIFGYWRMMRWNQERR.LLIEDLEARIALMPLFQAEKD.RTLQILREN..EEA
Retrocopy PGWGVSGWSVFSVGIGALIFGYWRMMRWNQERRSLLIEDLEARIALMPLFQAEKDQRTLQILREN-PEEA

Parental  IIMKDVPNWKVGESVFHTTRWVPPLIGEMYGLRTKEEMSNANFGFTWYT
          IIMKDVPN.KVGESVFH.TR..PPL..EMYGLRTK..M.NA.FGFTW.T
Retrocopy IIMKDVPNSKVGESVFHSTR*LPPLLDEMYGLRTKKYMNNASFGFTW*T

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	0.02 RPM	69.32 RPM
SRP007412_cerebellum	0.00 RPM	124.14 RPM
SRP007412_heart	0.16 RPM	250.63 RPM
SRP007412_kidney	0.04 RPM	171.90 RPM
SRP007412_liver	0.03 RPM	88.21 RPM
SRP007412_testis	0.00 RPM	72.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2453 was not detected

EST

No EST(s) were mapped for retro_mmus_2453 retrocopy.

TSS

No TSS is located nearby retro_mmus_2453 retrocopy 5' end.

Lab

retro_mmus_2453 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2453 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000034503	1 retrocopy	retro_cjac_262,
Mus musculus	ENSMUSG00000036199	1 retrocopy	retro_mmus_2453 ,
Rattus norvegicus	ENSRNOG00000020602	2 retrocopies	retro_rnor_210, retro_rnor_629,
Sorex araneus	ENSSARG00000004735	1 retrocopy	retro_sara_693,
Sus scrofa	ENSSSCG00000013936	3 retrocopies	retro_sscr_707, retro_sscr_722, retro_sscr_739,
Tursiops truncatus	ENSTTRG00000009880	1 retrocopy	retro_ttru_1141,