RetrogeneDB ID:

retro_cjac_2006

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:20:15360454..15360855(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000016062
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2006
GGTCCCTATGGACCACTCCAAAGTGTCCATAGTAGCCAAAAACCCTCCCGGCTTTGCTTTTGTTGAATTTGAAGATCCCC
GAGATACAGCTGATGCTGTCCGAGAGCTAGATGGAAGAACACTATGTGGCTGCCGTGTAAGAGTGGAACTGTCGAATGGT
GACAAAAGAAGTAGAAATCGTGGCCCACCTCCGTCTTGGGGCCGTCGTCCTCGAGATGATTATCGTTGGTGGAGTCCTCC
ACCTCGTCGCAGATCTCCAAGAAGAAGAAGCTTCTTTCGCAGCCGGAGCAGGTCCCTTTCTAGATAGGAGAAGAGAGAGA
TCGCTGTCTTGGGAGAGAAATTACAAGCCATCCCGATCCTTCTCTAGGTCTGGTAGCCGTTCTAGGTCAAATGAAAGGAA
A

ORF - retro_cjac_2006 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.24 %
Parental protein coverage: 81.71 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGYYGPLRSVW-VARNPPGFAFVEFEDPRDAADAVRELDGRTLCGCRVRVELSNGEKRSRNRGPPPSWGRR
G.YGPL.SV..VA.NPPGFAFVEFEDPRD.ADAVRELDGRTLCGCRVRVELSNG.KRSRNRGPPPSWGRR
RetrocopyGPYGPLQSVH>VAKNPPGFAFVEFEDPRDTADAVRELDGRTLCGCRVRVELSNGDKRSRNRGPPPSWGRR
ParentalPRDDYRRRSPPPRRRSPRRRSFSRSRSRSLSR-DRRRERSLSRERNHKPSRSFSRSRSRSRSNERK
PRDDYR..SPPPRRRSPRRRSF.RSRSRSLSR..RR.ERSLS.ERN.KPSRSFSRS.SRSRSNERK
RetrocopyPRDDYRWWSPPPRRRSPRRRSFFRSRSRSLSR>RRR-ERSLSWERNYKPSRSFSRSGSRSRSNERK

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 54 .80 RPM
SRP051959_heart 0 .00 RPM 44 .43 RPM
SRP051959_kidney 0 .00 RPM 56 .24 RPM
SRP051959_liver 0 .00 RPM 33 .10 RPM
SRP051959_lung 0 .00 RPM 56 .20 RPM
SRP051959_lymph_node 0 .00 RPM 68 .08 RPM
SRP051959_skeletal_muscle 0 .00 RPM 38 .65 RPM
SRP051959_spleen 0 .00 RPM 58 .24 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2006 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2006 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2006 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 25 parental genes, and 111 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000400065 retrocopies
Callithrix jacchus ENSCJAG000000011871 retrocopy
Callithrix jacchus ENSCJAG000000099713 retrocopies
Callithrix jacchus ENSCJAG00000016062 5 retrocopies
Dasypus novemcinctus ENSDNOG000000004219 retrocopies
Equus caballus ENSECAG000000187412 retrocopies
Echinops telfairi ENSETEG000000101172 retrocopies
Homo sapiens ENSG000001120814 retrocopies
Gorilla gorilla ENSGGOG000000171865 retrocopies
Loxodonta africana ENSLAFG000000181932 retrocopies
Microcebus murinus ENSMICG000000046745 retrocopies
Myotis lucifugus ENSMLUG000000106716 retrocopies
Macaca mulatta ENSMMUG000000143064 retrocopies
Mustela putorius furoENSMPUG000000142151 retrocopy
Mus musculus ENSMUSG000000711729 retrocopies
Oryctolagus cuniculus ENSOCUG000000066843 retrocopies
Otolemur garnettii ENSOGAG000000005026 retrocopies
Ochotona princeps ENSOPRG000000060063 retrocopies
Pan troglodytes ENSPTRG000000181064 retrocopies
Rattus norvegicus ENSRNOG0000000052011 retrocopies
Sus scrofa ENSSSCG000000015641 retrocopy
Ictidomys tridecemlineatus ENSSTOG000000142805 retrocopies
Tarsius syrichta ENSTSYG000000134983 retrocopies
Tursiops truncatus ENSTTRG0000001344711 retrocopies
Vicugna pacos ENSVPAG000000054811 retrocopy



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