RetrogeneDB ID:

retro_cjac_1081

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:13:32688457..32688958(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000002841
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:UBE2H
Ensembl ID:ENSCJAG00000010520
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1081
AAGCTCATTGAGAGTAAACATGAGGTTACGATCCTGGGAGGACTCAATGAATTTGTAGTGAAGTTTTATGGACCACAAGG
AACACCATATGAAGGCGGTGTATGGAAAGTTAGAGTGGACCTACCTGATAAATACCCTTTCAAATCTCCATCTATAGGAT
TCATGAATAAAATTTTGCATCCCAACATTGATGAAGCGTCAGGAACTCTGTGTCTAGATGTAATTAATCAAACTTGGACA
GCTCTCTATGATCTTACCAATATATTTGAGTCCTTCGGGCCCCAGTTTTTGGCCTATCCTAACCCTATAGATCCTCTCAA
TGGTGACGCTGCAGCCATGTACCTCCACCGACCAGAAGAATACAAGCAGAAAATTAAAGAGTACATCCAGAAATACGCCA
CGGAGGAGGCGCTGAAAGAGCAGGAAGAGGGCACCGGGGACAGCTCATTGGAAAGCTCTATGTCTGACTTTTCCGAAGAT
GAGGCCCAGGATATGGAGTTG

ORF - retro_cjac_1081 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.49 %
Parental protein coverage: 91.01 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKIFHPNIDEASGTV
KLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKI.HPNIDEASGT.
RetrocopyKLIESKHEVTILGGLNEFVVKFYGPQGTPYEGGVWKVRVDLPDKYPFKSPSIGFMNKILHPNIDEASGTL
ParentalCLDVINQTWTALYGNDLSDCFKNDGLPRVIVYKGEIDPDEITPNIICVYLARRELTFVEIKQYIQKYATE
CLDVINQTWTALY..DL...F...G.P....Y...IDP..........YL.R.E.....IK.YIQKYATE
RetrocopyCLDVINQTWTALY--DLTNIFESFG-PQFLAYPNPIDP--LNGDAAAMYLHRPEEYKQKIKEYIQKYATE
ParentalEALKEQEEGTGDSSSESSMSDFSEDEAQDMEL
EALKEQEEGTGDSS.ESSMSDFSEDEAQDMEL
RetrocopyEALKEQEEGTGDSSLESSMSDFSEDEAQDMEL

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 2 .60 RPM 7 .08 RPM
SRP051959_heart 3 .47 RPM 5 .82 RPM
SRP051959_kidney 4 .30 RPM 7 .70 RPM
SRP051959_liver 2 .32 RPM 4 .01 RPM
SRP051959_lung 4 .28 RPM 6 .75 RPM
SRP051959_lymph_node 2 .69 RPM 7 .44 RPM
SRP051959_skeletal_muscle 2 .27 RPM 4 .39 RPM
SRP051959_spleen 4 .52 RPM 8 .42 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1081 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1081 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1081 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 6 parental genes, and 8 retrocopies.

Species Parental gene accession Retrocopies number
Choloepus hoffmanni ENSCHOG000000036052 retrocopies
Callithrix jacchus ENSCJAG00000010520 1 retrocopy
retro_cjac_1081 ,
Homo sapiens ENSG000001865911 retrocopy
Nomascus leucogenys ENSNLEG000000126851 retrocopy
Pongo abelii ENSPPYG000000179971 retrocopy
Rattus norvegicus ENSRNOG000000482052 retrocopies



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