RetrogeneDB ID: retro_mmus_978

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 12:110319591..110319981(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Mrps26
• Ensembl ID: ENSMUSG00000037740
• Aliases: None
• Description: mitochondrial ribosomal protein S26 [Source:MGI Symbol;Acc:MGI:1333830]

Sequence

>retro_mmus_978
CTCAGGCTAGAGTTCACGTTGGAGGTGCGAAGGAAATTGCACGAGGCCCGAGCCGGGGTTCTGGCTGAGCGCAAGGCGCA
GCAGGCCATCACGGAGCACCGGGAGCTGATGGCCTAGAACCGGGATGAGAACCGGCGAATGCAGGAGCTACGGATAGCGA
GGTTGCAGCTGGAAGCACAGGCCCAGGAGGTGCAGAAGGCGGAGGCCCAGGCCCAGAGGGCCCAGGAGGAGCAGGCTTGG
GTGCAACTGAAAGAGCAAGAAGTGCTCAAGCTGCAGGAGGAGGCAAAAAACATCACTCAGGAGAACCTGGAGGCACGGAT
AGAAAAAGCGTTGGACTCTCCGAAGAGTTACAACTGGGCCACCACCAAAGAAGGGCAGGTGGTCAGGAAC

Alignment

ORF - retro_mmus_978 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.18 %
• Parental protein coverage: 65.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRLEFTLEVRRKLHEARAGVLAERKAQQAITEHRELMAWNRDENRRMQELRIARLQLEAQAQEVQKAEAQ
          LRLEFTLEVRRKLHEARAGVLAERKAQQAITEHRELMA.NRDENRRMQELRIARLQLEAQAQEVQKAEAQ
Retrocopy LRLEFTLEVRRKLHEARAGVLAERKAQQAITEHRELMA*NRDENRRMQELRIARLQLEAQAQEVQKAEAQ

Parental  AQRAQEEQAWVQLKEQEVLKLQEEAKNFITRENLEARIEEALDSPKSYNWAVTKEGQVVRN
          AQRAQEEQAWVQLKEQEVLKLQEEAKN.IT.ENLEARIE.ALDSPKSYNWA.TKEGQVVRN
Retrocopy AQRAQEEQAWVQLKEQEVLKLQEEAKN-ITQENLEARIEKALDSPKSYNWATTKEGQVVRN

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	29.69 RPM
SRP007412_cerebellum	0.00 RPM	24.14 RPM
SRP007412_heart	0.03 RPM	19.67 RPM
SRP007412_kidney	0.02 RPM	26.53 RPM
SRP007412_liver	0.00 RPM	14.47 RPM
SRP007412_testis	0.05 RPM	12.72 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_978 was not detected

EST

No EST(s) were mapped for retro_mmus_978 retrocopy.

TSS

No TSS is located nearby retro_mmus_978 retrocopy 5' end.

Lab

retro_mmus_978 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_978 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000024910	2 retrocopies	retro_dnov_2149, retro_dnov_780,
Felis catus	ENSFCAG00000028185	1 retrocopy	retro_fcat_843,
Loxodonta africana	ENSLAFG00000007936	1 retrocopy	retro_lafr_268,
Mus musculus	ENSMUSG00000037740	1 retrocopy	retro_mmus_978 ,
Nomascus leucogenys	ENSNLEG00000027041	1 retrocopy	retro_nleu_2813,