RetrogeneDB ID:

retro_cjac_2205

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:187080221..187080560(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000004633
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000003145
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2205
ATGGCGGTGGCAAATTCAAGCCCTGTTAACCCCGTGGTGTTCTTTGATGTCAGCATTGGCGGTCAGGAAGTTGGCCGCAT
GAAGATTGAGCTCTTCGCAGATGTTGTGCCTCAGACGGCCGAGAACTTTAGGCAGTTCTGCACTGGAGAATTCAGAAAAG
ATGGGATTCCAATAGGATACAAAGGAAGCACCTTCCACAGGGTCATAAAGGATTTCATGATTCAGGGTGGAGATTTCGTT
AATGGAGATGGTACTGGAGTCGCCAGTATTTACCGGGGGCCATTTGCAGATGAAAATTTTAAACTTAGTCACTCAGCTCC
AGGCCTGCTTTCTATGGCA

ORF - retro_cjac_2205 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 97.35 %
Parental protein coverage: 63.84 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPKTAENFRQFCTGEFRKDGVPIGYKGSTFHRVIK
MAVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVP.TAENFRQFCTGEFRKDG.PIGYKGSTFHRVIK
RetrocopyMAVANSSPVNPVVFFDVSIGGQEVGRMKIELFADVVPQTAENFRQFCTGEFRKDGIPIGYKGSTFHRVIK
ParentalDFMIQGGDFVNGDGTGVASIYRGPFADENFKLRHSAPGLLSMA
DFMIQGGDFVNGDGTGVASIYRGPFADENFKL.HSAPGLLSMA
RetrocopyDFMIQGGDFVNGDGTGVASIYRGPFADENFKLSHSAPGLLSMA

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 5 .77 RPM
SRP051959_heart 0 .02 RPM 4 .74 RPM
SRP051959_kidney 0 .00 RPM 6 .72 RPM
SRP051959_liver 0 .00 RPM 6 .19 RPM
SRP051959_lung 0 .03 RPM 7 .30 RPM
SRP051959_lymph_node 0 .00 RPM 8 .79 RPM
SRP051959_skeletal_muscle 0 .02 RPM 2 .64 RPM
SRP051959_spleen 0 .02 RPM 6 .49 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2205 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2205 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2205 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 24 parental genes, and 52 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000005261 retrocopy
Bos taurus ENSBTAG000000045901 retrocopy
Callithrix jacchus ENSCJAG00000003145 5 retrocopies
Callithrix jacchus ENSCJAG000000160941 retrocopy
Callithrix jacchus ENSCJAG000000196131 retrocopy
Cavia porcellus ENSCPOG000000082148 retrocopies
Dipodomys ordii ENSDORG000000161523 retrocopies
Homo sapiens ENSG000001719602 retrocopies
Gorilla gorilla ENSGGOG000000225072 retrocopies
Macropus eugenii ENSMEUG000000016911 retrocopy
Myotis lucifugus ENSMLUG000000254002 retrocopies
Macaca mulatta ENSMMUG000000131291 retrocopy
Mustela putorius furoENSMPUG000000139662 retrocopies
Mus musculus ENSMUSG000000602887 retrocopies
Nomascus leucogenys ENSNLEG000000123132 retrocopies
Oryctolagus cuniculus ENSOCUG000000114531 retrocopy
Otolemur garnettii ENSOGAG000000149371 retrocopy
Procavia capensis ENSPCAG000000111391 retrocopy
Pongo abelii ENSPPYG000000014672 retrocopies
Pan troglodytes ENSPTRG000000006142 retrocopies
Pteropus vampyrus ENSPVAG000000055001 retrocopy
Rattus norvegicus ENSRNOG000000084891 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000001152 retrocopies
Tarsius syrichta ENSTSYG000000031822 retrocopies



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