RetrogeneDB ID:

retro_mmus_3636

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:74494381..74494822(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000083283
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ube2d3
Ensembl ID:ENSMUSG00000078578
Aliases:Ube2d3, 1100001F19Rik, 9430029A22Rik, AA414951
Description:ubiquitin-conjugating enzyme E2D 3 [Source:MGI Symbol;Acc:MGI:1913355]


Retrocopy-Parental alignment summary:






>retro_mmus_3636
ATGGCGCTGAAACGGATTAATAAGGAACTTAGTGATTTGGCCCGTGACCCTCCAGCACAATGCTCCGCAGGTCCAGTTGG
AGATGACATGTTTCATTGGCAAGCCACAATTATGGGACCTAATGACAGCCCATATAAAAGTGGTGTAATCTTTTTGACAA
TTCATTTTCCTACAGACTACCCCTTCAAACCACCTAAGGTTGCATTTACAACAAGAATTTATCATCCAAATATTAACAGT
AATGGCAGCATTTGTCTTGATATTCTAAGATCACAGTGGTCTCCTGCTTTAACTATTTCCAAAGTTCTTTTATCCATTCG
TTCACTGCTATGTGATCCAAACCCAGATGACCCCCTAGTGCCAGAGATTGCATGGATCTATAATACAGACAGAGATAAGT
ACAACAGAAGATCTTGGGAATGGGCTCAGAAGTATACCGTA

ORF - retro_mmus_3636 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.52 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYQGGVFFLTIHFPTDYPFKPPKVAFT
MALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPY..GV.FLTIHFPTDYPFKPPKVAFT
RetrocopyMALKRINKELSDLARDPPAQCSAGPVGDDMFHWQATIMGPNDSPYKSGVIFLTIHFPTDYPFKPPKVAFT
ParentalTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSICSLLCDPNPDDPLVPEIARIYKTDRDKYNRISRE
TRIYHPNINSNGSICLDILRSQWSPALTISKVLLSI.SLLCDPNPDDPLVPEIA.IY.TDRDKYNR.S.E
RetrocopyTRIYHPNINSNGSICLDILRSQWSPALTISKVLLSIRSLLCDPNPDDPLVPEIAWIYNTDRDKYNRRSWE
ParentalWTQKYAM
W.QKY..
RetrocopyWAQKYTV

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 .02 RPM 96 .68 RPM
SRP007412_cerebellum 0 .00 RPM 65 .26 RPM
SRP007412_heart 0 .06 RPM 135 .32 RPM
SRP007412_kidney 0 .02 RPM 106 .26 RPM
SRP007412_liver 0 .05 RPM 106 .78 RPM
SRP007412_testis 0 .00 RPM 71 .76 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_3636 was not detected
No EST(s) were mapped for retro_mmus_3636 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_157978532 libraries453 libraries82 libraries1 library4 libraries

The graphical summary, for retro_mmus_3636 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_3636 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3636 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 19 parental genes, and 85 retrocopies.

Species Parental gene accession Retrocopies number
Ciona intestinalis ENSCING000000187112 retrocopies
Ciona savignyi ENSCSAVG000000061361 retrocopy
Erinaceus europaeus ENSEEUG000000146583 retrocopies
Echinops telfairi ENSETEG000000012913 retrocopies
Felis catus ENSFCAG000000249182 retrocopies
Gorilla gorilla ENSGGOG000000013682 retrocopies
Mus musculus ENSMUSG0000001992722 retrocopies
Mus musculus ENSMUSG000000217743 retrocopies
Mus musculus ENSMUSG000000270114 retrocopies
Mus musculus ENSMUSG0000003896510 retrocopies
Mus musculus ENSMUSG00000078578 11 retrocopies
Mus musculus ENSMUSG000000918963 retrocopies
Ornithorhynchus anatinus ENSOANG000000054151 retrocopy
Pongo abelii ENSPPYG000000149671 retrocopy
Pteropus vampyrus ENSPVAG000000154381 retrocopy
Sus scrofa ENSSSCG000000243061 retrocopy
Sus scrofa ENSSSCG000000298224 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000134816 retrocopies
Tupaia belangeri ENSTBEG000000002705 retrocopies



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