RetrogeneDB ID:

retro_mmus_894

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:12:106459228..106459499(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000091762
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
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]


Retrocopy-Parental alignment summary:






>retro_mmus_894
ATGGGACTAGAAGATCAACGAAAGATGCTCACTGGATCTGGAGACCCCCAAAGAGGAAGAAGAGGAGAAAGAATTGGTGG
ACACCCTAACAACAGTGAGAGAGCACCTTGTGCAGTTGGGGAAGTGTGTAAAAGCCCAGGAATGTCTAGAGTTGTGTGAT
AAGCGCGTGTCTTCCAGATCACAGACAGAAGAGGATTGTACAGAGGAGCTCTTCGACTTTGTGCATGCACGGAACCACTG
TGTGGCCCCCAAACTCTCGAAAAGCTTGAAG

ORF - retro_mmus_894 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.52 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMGLEDERKMLTGSGDP-KEEEEE-ELVDPLTTVREHCEQLEKCVKARERLELCDNRVSSRSQTEEDCTEE
MGLED.RKMLTGSGDP.KEEEEE.ELVD.LTTVREH..QL.KCVKA.E.LELCD.RVSSRSQTEEDCTEE
RetrocopyMGLEDQRKMLTGSGDP>KEEEEEKELVDTLTTVREHLVQLGKCVKAQECLELCDKRVSSRSQTEEDCTEE
ParentalLFDFLHARDHCVAHKLFKNLK
LFDF.HAR.HCVA.KL.K.LK
RetrocopyLFDFVHARNHCVAPKLSKSLK

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)

Expression validation based on RNA-Seq data:
Library Retrocopy expression Parental gene expression
SRP007412_brain 0 .00 RPM 100 .67 RPM
SRP007412_cerebellum 0 .00 RPM 77 .16 RPM
SRP007412_heart 0 .00 RPM 262 .86 RPM
SRP007412_kidney 0 .00 RPM 180 .12 RPM
SRP007412_liver 0 .00 RPM 87 .74 RPM
SRP007412_testis 1 .05 RPM 33 .62 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_894 was not detected
No EST(s) were mapped for retro_mmus_894 retrocopy.


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_20903308 libraries120 libraries87 libraries204 libraries353 libraries

The graphical summary, for retro_mmus_894 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)

retro_mmus_894 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_894 has 0 orthologous retrocopies within eutheria group .


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

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000096033 retrocopies
Callithrix jacchus ENSCJAG000000211265 retrocopies
Homo sapiens ENSG000001736605 retrocopies
Gorilla gorilla ENSGGOG000000106311 retrocopy
Macropus eugenii ENSMEUG000000068501 retrocopy
Mus musculus ENSMUSG00000063882 4 retrocopies
Nomascus leucogenys ENSNLEG000000165234 retrocopies
Oryctolagus cuniculus ENSOCUG000000076001 retrocopy
Otolemur garnettii ENSOGAG000000011342 retrocopies
Ochotona princeps ENSOPRG000000160591 retrocopy
Pongo abelii ENSPPYG000000258314 retrocopies
Pan troglodytes ENSPTRG000000006914 retrocopies
Rattus norvegicus ENSRNOG000000125501 retrocopy
Sorex araneus ENSSARG000000067631 retrocopy
Tupaia belangeri ENSTBEG000000116082 retrocopies
Tarsius syrichta ENSTSYG000000065722 retrocopies
Tursiops truncatus ENSTTRG000000063261 retrocopy



Copyright © RetrogeneDB 2014-2017