RetrogeneDB ID:

retro_cjac_1180

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:4612326..4612587(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2A
Ensembl ID:ENSCJAG00000005098
Aliases:None
Description:ubiquitin-conjugating enzyme E2A [Source:HGNC Symbol;Acc:12472]


Retrocopy-Parental alignment summary:






>retro_cjac_1180
ATGTCCACCCCGGCTCGCCGGCGCCTCATGCGGGACTTCAAGAGGTTGCAGGAGGATCCTCCAGCCAGAGTCAGCGGGGC
TCCGTCCGAGAACAACATAATGGTGTGAAACGCGGTCATTTTCGGGCCTGAAGGGACCCCATTTGAGGATGGAACATTTA
AACTTACAACAGAGATCACTAAAGAATATCCAAATAAGCCACCTACTGTTAGATTTGTCTCTAAGATGTTCCATCCAAAT
GTCTATGCAGACGGTAGTATA

ORF - retro_cjac_1180 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 94.25 %
Parental protein coverage: 57.24 %
Number of stop codons detected: 1
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSTPARRRLMRDFKRLQEDPPAGVSGAPSENNIMVWNAVIFGPEGTPFEDGTFKLTIEFTEEYPNKPPTV
MSTPARRRLMRDFKRLQEDPPA.VSGAPSENNIMV.NAVIFGPEGTPFEDGTFKLT.E.T.EYPNKPPTV
RetrocopyMSTPARRRLMRDFKRLQEDPPARVSGAPSENNIMV*NAVIFGPEGTPFEDGTFKLTTEITKEYPNKPPTV
ParentalRFVSKMFHPNVYADGSI
RFVSKMFHPNVYADGSI
RetrocopyRFVSKMFHPNVYADGSI

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 9 .65 RPM
SRP051959_heart 0 .00 RPM 9 .00 RPM
SRP051959_kidney 0 .00 RPM 12 .00 RPM
SRP051959_liver 0 .02 RPM 6 .54 RPM
SRP051959_lung 0 .00 RPM 11 .06 RPM
SRP051959_lymph_node 0 .00 RPM 10 .16 RPM
SRP051959_skeletal_muscle 0 .00 RPM 13 .50 RPM
SRP051959_spleen 0 .00 RPM 10 .00 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1180 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1180 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1180 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000010791 retrocopy
Callithrix jacchus ENSCJAG000000008743 retrocopies
Callithrix jacchus ENSCJAG00000005098 2 retrocopies
retro_cjac_1180 , retro_cjac_3862,
Cavia porcellus ENSCPOG000000119081 retrocopy
Dasypus novemcinctus ENSDNOG000000070601 retrocopy
Macropus eugenii ENSMEUG000000030261 retrocopy
Monodelphis domestica ENSMODG000000102091 retrocopy
Oryctolagus cuniculus ENSOCUG000000167391 retrocopy
Otolemur garnettii ENSOGAG000000243351 retrocopy
Procavia capensis ENSPCAG000000050451 retrocopy
Sus scrofa ENSSSCG000000126211 retrocopy
Tarsius syrichta ENSTSYG000000008881 retrocopy



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