RetrogeneDB ID:

retro_cjac_3140

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:8:60488116..60488554(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2V1
Ensembl ID:ENSCJAG00000036984
Aliases:None
Description:ubiquitin-conjugating enzyme E2 variant 1 [Source:RefSeq peptide;Acc:NP_001192018]


Retrocopy-Parental alignment summary:






>retro_cjac_3140
GCAGCCACCACAGGCTCAGGAGTAAAAGTCCTTCGCAATTTCTAACTGTTGCTAGAACTCAAATAAGGCCAGAAAGGAGT
AGGAGATGGCACAATTAGCTGGGATTTAGATGGTAACAAGACATGACACTCAAAAGATGAACAGGGATGATAATTGCGCC
TCCAAGAACAATTTATGAAAACCAAATATGCAGCCTTAAAATAGAATGTGGACCTAAATACCCAGAAGCACCCTCCTTTG
TCAGATTTGTAACAAAAATCAATATGAATGGAGTTAATAGTTCTAATGGAGTGGTGGACCCAAGAGCCATATCAGTGCTA
GCAAAATGGCAAAATACATATAGCATTAAAGTTGTCCTGCAAGAGCTTCAGTGCCTTAATTATGTCTAAACAAAATATGA
AACTCCCTCAGTCGCCTGAAGGACAGTGTTACAGCAAC

ORF - retro_cjac_3140 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.11 %
Parental protein coverage: 99.32 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalAATTGSGVKVPRNFRLLEELEEGQKGVGDGTVSWGLEDD-EDMTLTRWTGMIIGPPRTIYENRIYSLKIE
AATTGSGVKV.RNF.LL.EL..GQKGVGDGT.SW.L.....DMTL.R.TGMII.PPRTIYEN.I.SLKIE
RetrocopyAATTGSGVKVLRNF*LLLELK*GQKGVGDGTISWDLDGN<QDMTLKR*TGMIIAPPRTIYENQICSLKIE
ParentalCGPKYPEAPPFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNSYSIKVVLQELR-RLMMSKENMKLPQP
CGPKYPEAP.FVRFVTKINMNGVNSSNGVVDPRAISVLAKWQN.YSIKVVLQEL...L.MSK.NMKLPQ.
RetrocopyCGPKYPEAPSFVRFVTKINMNGVNSSNGVVDPRAISVLAKWQNTYSIKVVLQELQ>ALIMSKQNMKLPQS
ParentalPEGQCYSN
PEGQCYSN
RetrocopyPEGQCYSN

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
SRP051959_colon 0 .35 RPM 5 .24 RPM
SRP051959_heart 0 .33 RPM 5 .47 RPM
SRP051959_kidney 0 .78 RPM 7 .65 RPM
SRP051959_liver 0 .26 RPM 5 .65 RPM
SRP051959_lung 0 .37 RPM 7 .40 RPM
SRP051959_lymph_node 0 .23 RPM 7 .72 RPM
SRP051959_skeletal_muscle 0 .20 RPM 6 .97 RPM
SRP051959_spleen 0 .34 RPM 7 .18 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3140 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3140 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3140 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Macaca mulatta retro_mmul_1722

Parental genes homology:
Parental genes homology involve 14 parental genes, and 83 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000273164 retrocopies
Callithrix jacchus ENSCJAG000000321821 retrocopy
Callithrix jacchus ENSCJAG00000036984 10 retrocopies
Homo sapiens ENSG000002446874 retrocopies
Loxodonta africana ENSLAFG000000273592 retrocopies
Macaca mulatta ENSMMUG000000122286 retrocopies
Mustela putorius furoENSMPUG000000175573 retrocopies
Nomascus leucogenys ENSNLEG000000069878 retrocopies
Oryctolagus cuniculus ENSOCUG000000261724 retrocopies
Otolemur garnettii ENSOGAG0000002589412 retrocopies
Pan troglodytes ENSPTRG000000136151 retrocopy
Rattus norvegicus ENSRNOG0000002558021 retrocopies
Sus scrofa ENSSSCG000000306321 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000143226 retrocopies



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