RetrogeneDB ID: retro_mmus_3675

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: X:101691547..101691850(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000082729
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Vma21
• Ensembl ID: ENSMUSG00000073131
• Aliases: Vma21, 2610030H06Rik, AI840175
• Description: VMA21 vacuolar H+-ATPase homolog (S. cerevisiae) [Source:MGI Symbol;Acc:MGI:1914298]

Sequence

>retro_mmus_3675
ATGGAGCGTCTTGATAAAGCAGCGCTGAATGCGCTGCAGCCTCCAGAGTTCAGAAATGAAAACTCTTTAGCTGCAACCCT
GAAGACACTGCTGTTCTTCACAGCTTTAATGATCACGGTTCCTATCGGCTTGTATTTTACAACGAAAGCTTATATATTTG
GAGGTGCCCTTGGAATGTCTAATAGAGACAGCTATTTTTATGCCGCAATTGTTGCTGTTGTTGCTGTTCATGTGGTTCTG
GCCCTGTTTGTCTATGTGGCCTGGAATGAAGGCTCACGACAGTGGCGTGAAGGCAAACAGGAT

Alignment

ORF - retro_mmus_3675 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.08 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERLDKAALNALQPPEFRNENSLAATLKTLLFFTALMITVPIGLYFTTKAYIFEGALGMSNRDSYFYAAI
          MERLDKAALNALQPPEFRNENSLAATLKTLLFFTALMITVPIGLYFTTKAYIF.GALGMSNRDSYFYAA.
Retrocopy MERLDKAALNALQPPEFRNENSLAATLKTLLFFTALMITVPIGLYFTTKAYIFGGALGMSNRDSYFYAAX

Parental  VAVVAVHVVLALFVYVAWNEGSRQWREGKQD
          ......HVVLALFVYVAWNEGSRQWREGKQD
Retrocopy XXXXXXHVVLALFVYVAWNEGSRQWREGKQD

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	0.00 RPM	27.03 RPM
SRP007412_cerebellum	0.00 RPM	26.31 RPM
SRP007412_heart	0.00 RPM	5.70 RPM
SRP007412_kidney	0.02 RPM	16.82 RPM
SRP007412_liver	0.00 RPM	15.54 RPM
SRP007412_testis	0.00 RPM	1.74 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_3675 was not detected

EST

No EST(s) were mapped for retro_mmus_3675 retrocopy.

TSS

No TSS is located nearby retro_mmus_3675 retrocopy 5' end.

Lab

retro_mmus_3675 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_3675 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006296	1 retrocopy	retro_btau_1106,
Callithrix jacchus	ENSCJAG00000003916	1 retrocopy	retro_cjac_150,
Dasypus novemcinctus	ENSDNOG00000008426	1 retrocopy	retro_dnov_504,
Echinops telfairi	ENSETEG00000006467	1 retrocopy	retro_etel_528,
Homo sapiens	ENSG00000160131	1 retrocopy	retro_hsap_3724,
Macaca mulatta	ENSMMUG00000009034	1 retrocopy	retro_mmul_1693,
Mus musculus	ENSMUSG00000073131	2 retrocopies	retro_mmus_116, retro_mmus_3675 ,
Nomascus leucogenys	ENSNLEG00000013711	1 retrocopy	retro_nleu_1971,
Oryctolagus cuniculus	ENSOCUG00000015201	1 retrocopy	retro_ocun_443,
Pongo abelii	ENSPPYG00000020820	1 retrocopy	retro_pabe_3133,
Pan troglodytes	ENSPTRG00000022372	1 retrocopy	retro_ptro_2521,
Rattus norvegicus	ENSRNOG00000049744	1 retrocopy	retro_rnor_2843,
Ictidomys tridecemlineatus	ENSSTOG00000011179	1 retrocopy	retro_itri_500,