RetrogeneDB ID:

retro_rnor_650

Retrocopy
location
Organism:Rat (Rattus norvegicus)
Coordinates:1:248496034..248496310(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:Ube2d3
Ensembl ID:ENSRNOG00000013741
Aliases:None
Description:ubiquitin-conjugating enzyme E2 D3 [Source:RefSeq peptide;Acc:NP_112516]


Retrocopy-Parental alignment summary:






>retro_rnor_650
ATTCGATTTTCTACAGACTACCCCTCTAAACGACCTAAGGTTTTATGTACAAGAATTGATTATCCAAATAGTAACAGTAA
TGGCAGCATTTATCTATTATTATTCTCAGATCACAGTGTCTCTGCTTTAACATGTCTAAAGTTCTCTTATCCATTTGTTC
ACTGCTATGTGATCCAACCCCAACTGATCTTTAGCACCAGAGATTGCTCAGATCTAAAACGTGACAAAGATAAATACAAC
AGAATATGTCTGGACTGGGCTTAGCAATATGCCATG

ORF - retro_rnor_650 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.82 %
Parental protein coverage: 63.95 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalIHFPTDYPFKPPKVAFTTRIYHPNINSNGSICLDILRSQWSPALT-ISKVLLSICSLLCDPNPDD-PLVP
I.F.TDYP.K.PKV...TRI..PN.NSNGSI.L.........ALT..SKVLLSICSLLCDP.P.D..L.P
RetrocopyIRFSTDYPSKRPKV-LCTRIDYPNSNSNGSIYLLLFSDHSVSALT<MSKVLLSICSLLCDPTPTD<SLAP
ParentalEIARI-YKTDRDKYNRISREWTQKYAM
EIA.I..K.D.DKYNRI...W...YAM
RetrocopyEIAQI<LKRDKDKYNRICLDWA*QYAM

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
SRP017611_brain 0 .00 RPM 133 .66 RPM
SRP017611_kidney 0 .00 RPM 209 .77 RPM
SRP017611_liver 0 .00 RPM 130 .51 RPM
Rattus norvegicus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_rnor_650 retrocopy.
Rattus norvegicus was not studied using FANTOM5 data.
retro_rnor_650 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_rnor_650 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 18 parental genes, and 86 retrocopies.

Species Parental gene accession Retrocopies number
Ciona intestinalis ENSCING000000187112 retrocopies
Ciona savignyi ENSCSAVG000000061361 retrocopy
Dasypus novemcinctus ENSDNOG0000000932030 retrocopies
Erinaceus europaeus ENSEEUG000000146583 retrocopies
Echinops telfairi ENSETEG000000012913 retrocopies
Gorilla gorilla ENSGGOG000000013682 retrocopies
Ornithorhynchus anatinus ENSOANG000000054151 retrocopy
Ochotona princeps ENSOPRG000000116959 retrocopies
Pongo abelii ENSPPYG000000149671 retrocopy
Pteropus vampyrus ENSPVAG000000154381 retrocopy
Rattus norvegicus ENSRNOG000000018624 retrocopies
Rattus norvegicus ENSRNOG000000045441 retrocopy
Rattus norvegicus ENSRNOG000000087943 retrocopies
Rattus norvegicus ENSRNOG00000013741 9 retrocopies
Sus scrofa ENSSSCG000000243061 retrocopy
Sus scrofa ENSSSCG000000298224 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000134816 retrocopies
Tupaia belangeri ENSTBEG000000002705 retrocopies



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