RetrogeneDB ID:

retro_cjac_3882

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL285783.1:39621..39861(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2D4
Ensembl ID:ENSCJAG00000007875
Aliases:None
Description:ubiquitin-conjugating enzyme E2D 4 (putative) [Source:HGNC Symbol;Acc:21647]


Retrocopy-Parental alignment summary:






>retro_cjac_3882
TTTCTTCCTGACCATCCACTTGCCTACGGATTCAAGCCCCCAAAGGTTGCTTTCACAGCCAGATTTTCTCACCCCAGTGT
CAACAGTAATGACAGCATCTGCCGTGACAGCCTGTGGTCTCAGTGGTCTCCAGCATTGACTGTGTCAAAAGTTCTCTTGT
CTATCTGCTCACTGCTCTGCACCCCCAACCTCGATGACCCTCTGGTGCCAGAGATAGCCCGCACTTACCAGGCCGGCAGA

ORF - retro_cjac_3882 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 72.84 %
Parental protein coverage: 55.1 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFLTIHFPTDYPFKPPKVAFTTKIYHPNINSNGSICLDILRSQWSPALTVSKVLLSICSLLCDPNPDDPLV
FL..H.P..Y.FKPPKVAFT....HP..NSN.SIC.D.L.SQWSPALTVSKVLLSICSLLC.PN.DDPLV
RetrocopyFLPDH-PLAYGFKPPKVAFTARFSHPSVNSNDSICRDSLWSQWSPALTVSKVLLSICSLLCTPNLDDPLV
ParentalPEVAHTYKADR
PE.A.TY.A.R
RetrocopyPEIARTYQAGR

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 .00 RPM 2 .13 RPM
SRP051959_heart 0 .02 RPM 9 .98 RPM
SRP051959_kidney 0 .00 RPM 9 .34 RPM
SRP051959_liver 0 .00 RPM 6 .19 RPM
SRP051959_lung 0 .00 RPM 5 .45 RPM
SRP051959_lymph_node 0 .00 RPM 3 .68 RPM
SRP051959_skeletal_muscle 0 .00 RPM 25 .16 RPM
SRP051959_spleen 0 .02 RPM 4 .50 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3882 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3882 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3882 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 16 parental genes, and 68 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000039971 retrocopy
Callithrix jacchus ENSCJAG00000007875 4 retrocopies
Callithrix jacchus ENSCJAG000000115593 retrocopies
Callithrix jacchus ENSCJAG000000154923 retrocopies
Callithrix jacchus ENSCJAG000000158189 retrocopies
Dipodomys ordii ENSDORG000000068885 retrocopies
Homo sapiens ENSG000000789672 retrocopies
Gorilla gorilla ENSGGOG000000033783 retrocopies
Myotis lucifugus ENSMLUG000000119193 retrocopies
Macaca mulatta ENSMMUG000000024105 retrocopies
Nomascus leucogenys ENSNLEG000000033643 retrocopies
Oryctolagus cuniculus ENSOCUG000000089001 retrocopy
Pongo abelii ENSPPYG000000297271 retrocopy
Sus scrofa ENSSSCG000000167222 retrocopies
Tupaia belangeri ENSTBEG000000036919 retrocopies
Tarsius syrichta ENSTSYG0000000059514 retrocopies



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