RetrogeneDB ID:

retro_mmus_3406

Retrocopy
location
Organism:Mouse (Mus musculus)
Coordinates:X:3486592..3486819(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSMUSG00000082167
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:Ube2d1
Ensembl ID:ENSMUSG00000019927
Aliases:Ube2d1, UBCH5
Description:ubiquitin-conjugating enzyme E2D 1 [Source:MGI Symbol;Acc:MGI:2384911]


Retrocopy-Parental alignment summary:






>retro_mmus_3406
TTTTTGACAAATCAGTTTCCTTTAGACTACACCTTCAAGCCACTTAAGGTTGCGTTTACAACAAAAATTTATCATCTAAA
TATCAACAGTAATGGCAGCATTTATCTTGATAATCTCAGATCACAGTGTCTCCTGCTTTAACTATTTCTAATGTTCATTT
ATCCATTTGTTCACTGCTATGTGATCCAAACCCTGATGACCTCCTAGTGCCAGAGACTGCACAGATC

ORF - retro_mmus_3406 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 77.92 %
Parental protein coverage: 51.7 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalFLTVHFPTDYPFKPPKIAFTTKIYHPNINSNGSICLDILRSQW-SPALTVSKVLLSICSLLCDPNPDDPL
FLT..FP.DY.FKP.K.AFTTKIYH.NINSNGSI.LD.LRSQ..SPALT.S.V.LSICSLLCDPNPDD.L
RetrocopyFLTNQFPLDYTFKPLKVAFTTKIYHLNINSNGSIYLDNLRSQC<SPALTISNVHLSICSLLCDPNPDDLL
ParentalVPDIAQI
VP..AQI
RetrocopyVPETAQI

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 37 .33 RPM
SRP007412_cerebellum 0 .00 RPM 33 .35 RPM
SRP007412_heart 0 .00 RPM 24 .25 RPM
SRP007412_kidney 0 .00 RPM 17 .19 RPM
SRP007412_liver 0 .00 RPM 5 .98 RPM
SRP007412_testis 0 .00 RPM 3 .52 RPM
RNA Polymerase II actvity near the 5' end of retro_mmus_3406 was not detected
No EST(s) were mapped for retro_mmus_3406 retrocopy.
No TSS is located nearby retro_mmus_3406 retrocopy 5' end.
retro_mmus_3406 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_mmus_3406 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 20 parental genes, and 119 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000207965 retrocopies
Choloepus hoffmanni ENSCHOG0000000121321 retrocopies
Dasypus novemcinctus ENSDNOG000000138211 retrocopy
Echinops telfairi ENSETEG000000022802 retrocopies
Homo sapiens ENSG000000724012 retrocopies
Macropus eugenii ENSMEUG000000072381 retrocopy
Microcebus murinus ENSMICG000000102531 retrocopy
Myotis lucifugus ENSMLUG0000000571013 retrocopies
Mus musculus ENSMUSG00000019927 22 retrocopies
Mus musculus ENSMUSG000000217743 retrocopies
Mus musculus ENSMUSG000000270114 retrocopies
Mus musculus ENSMUSG0000003896510 retrocopies
Mus musculus ENSMUSG0000007857811 retrocopies
Mus musculus ENSMUSG000000918963 retrocopies
Procavia capensis ENSPCAG000000069981 retrocopy
Pteropus vampyrus ENSPVAG000000073942 retrocopies
Sarcophilus harrisii ENSSHAG000000104811 retrocopy
Tarsius syrichta ENSTSYG000000112293 retrocopies
Tursiops truncatus ENSTTRG000000092448 retrocopies
Vicugna pacos ENSVPAG000000069445 retrocopies



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