RetrogeneDB ID: retro_mmus_1965

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 2:119008208..119008474(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000081413
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Uqcrh
• Ensembl ID: ENSMUSG00000063882
• Aliases: Uqcrh, 2210416J04Rik, 2310021J10Rik, 2610041P16Rik
• Description: ubiquinol-cytochrome c reductase hinge protein [Source:MGI Symbol;Acc:MGI:1913826]

Sequence

>retro_mmus_1965
ATGGGACTAGAGGATGAACGAAAGATGCTCACTGGATCCGGAGACCCCAACGAGGAAGAAGAGGAAGAATTAGTGGGCCC
CCTAACAACAGTGAGAGAGCACTGTGAACCGCTGGAGAAGTGTGTAAAGGCCCGGGAATGACCAGAGTTGTGTGATAATC
CGTGTCTTCCCGATCACAGACAGGAGAGGATTGTACAGAGGAGCTCTTTGGCTTCTTGCACTCACGGGACCACTGTGTGG
CCCACAAGCTCTTTAAAAACTTGAAG

Alignment

ORF - retro_mmus_1965 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.89 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGLEDERKMLTGSGDPKEEEEEELVDPLTTVREHCEQLEKCVKARERLELCDN-RVSSRSQTEEDCTEEL
          MGLEDERKMLTGSGDP.EEEEEELV.PLTTVREHCE.LEKCVKARE..ELCDN..VSSRSQT.EDCTEEL
Retrocopy MGLEDERKMLTGSGDPNEEEEEELVGPLTTVREHCEPLEKCVKARE*PELCDN<SVSSRSQTGEDCTEEL

Parental  FDFLHARDHCVAHKLFKNLK
          F.FLH.RDHCVAHKLFKNLK
Retrocopy FGFLHSRDHCVAHKLFKNLK

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	100.67 RPM
SRP007412_cerebellum	0.04 RPM	77.16 RPM
SRP007412_heart	0.16 RPM	262.86 RPM
SRP007412_kidney	0.29 RPM	180.12 RPM
SRP007412_liver	0.05 RPM	87.74 RPM
SRP007412_testis	0.00 RPM	33.62 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_1965 was not detected

EST

No EST(s) were mapped for retro_mmus_1965 retrocopy.

TSS

TSS No.	TSS Name	TSS expression level (Expr) in TPM range:
		no expression	0 < Expr ≤ 1	1 < Expr ≤ 5	5 < Expr ≤ 10	Expr > 10
TSS #1	TSS_79173	308 libraries	534 libraries	221 libraries	8 libraries	1 library

The graphical summary, for retro_mmus_1965 TSS expression levels > 0 TPM .
TSS expression levels were studied across 1072 TSS-CAGE libraries, based on FANTOM5 data.
The expression values were visualized using beanplot. If you have any doubts, how to read it, read more in Kampstra P (2008)

Lab

retro_mmus_1965 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1965 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 17 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009603	3 retrocopies	retro_btau_1247, retro_btau_691, retro_btau_732,
Callithrix jacchus	ENSCJAG00000021126	5 retrocopies	retro_cjac_1303, retro_cjac_1337, retro_cjac_2726, retro_cjac_3338, retro_cjac_962,
Homo sapiens	ENSG00000173660	5 retrocopies	retro_hsap_2085, retro_hsap_2659, retro_hsap_3200, retro_hsap_348, retro_hsap_564,
Gorilla gorilla	ENSGGOG00000010631	1 retrocopy	retro_ggor_1855,
Macropus eugenii	ENSMEUG00000006850	1 retrocopy	retro_meug_1932,
Mus musculus	ENSMUSG00000063882	4 retrocopies	retro_mmus_1426, retro_mmus_1965 , retro_mmus_2126, retro_mmus_894,
Nomascus leucogenys	ENSNLEG00000016523	4 retrocopies	retro_nleu_1152, retro_nleu_1529, retro_nleu_2134, retro_nleu_2212,
Oryctolagus cuniculus	ENSOCUG00000007600	1 retrocopy	retro_ocun_1410,
Otolemur garnettii	ENSOGAG00000001134	2 retrocopies	retro_ogar_487, retro_ogar_763,
Ochotona princeps	ENSOPRG00000016059	1 retrocopy	retro_opri_489,
Pongo abelii	ENSPPYG00000025831	4 retrocopies	retro_pabe_2314, retro_pabe_2653, retro_pabe_516, retro_pabe_7,
Pan troglodytes	ENSPTRG00000000691	4 retrocopies	retro_ptro_1534, retro_ptro_1792, retro_ptro_2246, retro_ptro_422,
Rattus norvegicus	ENSRNOG00000012550	1 retrocopy	retro_rnor_1227,
Sorex araneus	ENSSARG00000006763	1 retrocopy	retro_sara_110,
Tupaia belangeri	ENSTBEG00000011608	2 retrocopies	retro_tbel_1692, retro_tbel_2458,
Tarsius syrichta	ENSTSYG00000006572	2 retrocopies	retro_tsyr_1821, retro_tsyr_2156,
Tursiops truncatus	ENSTTRG00000006326	1 retrocopy	retro_ttru_622,