RetrogeneDB ID:

retro_cjac_3707

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01196462.1:1339..1807(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RAP1A
Ensembl ID:ENSCJAG00000013392
Aliases:None
Description:RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]


Retrocopy-Parental alignment summary:






>retro_cjac_3707
TTTTTTTTTAAATATTACCCAATGATAGAAATTTCCTAAAGAAAGCAAGTTGCAGTGGATTAACAACAGTGTATTCTAGA
AATTCTGGATACTGCAGGGACAGAGCAATTTACAGCGATGAGGAATTTGTATATGAAGAATGGACAAGGTTTAACACTAG
TATATTCTGTTATAGCTCAATCCACATTTAATGACTTACAGGACCTGAGGGAACATATTTTATGTGTTAAGGGCACAGAA
GATGTTCCAGTGATTTTGGATGGCAATAAATGTGACCTGGAAGATGAGCGAGTAGTTGGCAAAGAACAGCGCCGGAATTT
GGCAAGACAATAGTGTAACTGCGCCTTTGTAGAAACTTCTGCAAAGTCAAAGATCAATGTTATTGATCTTTGTGACCTGA
TAAGACAGATAAATAGAAAAATGCTAGTGGAAAAGAAGAATCCTAAAAAGAAATCATGTCTGCTGCTC

ORF - retro_cjac_3707 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.98 %
Parental protein coverage: 85.33 %
Number of stop codons detected: 3
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFVEKYDPTIEDSYRKQVEVDCQQCMLEILDTAGTEQFTAMRDLYMKNGQGFALVYSITAQSTFNDLQDLR
F..KY.P.IE.S.RKQV.VD.QQC.LEILDTAGTEQFTAMR.LYMKNGQG..LVYS..AQSTFNDLQDLR
RetrocopyFFFKYYPMIEIS*RKQVAVD*QQCILEILDTAGTEQFTAMRNLYMKNGQGLTLVYSVIAQSTFNDLQDLR
ParentalEQILRVKDTEDVPMILVGNKCDLEDERVVGKEQGQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINR
E.IL.VK.TEDVP.IL.GNKCDLEDERVVGKEQ..NLARQ.CNCAF.E.SAKSKINV.....DL.RQINR
RetrocopyEHILCVKGTEDVPVILDGNKCDLEDERVVGKEQRRNLARQ*CNCAFVETSAKSKINVIDL-CDLIRQINR
ParentalKTPVEKKKPKKKSCLLL
K..VEKK.PKKKSCLLL
RetrocopyKMLVEKKNPKKKSCLLL

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 16 .55 RPM
SRP051959_heart 0 .00 RPM 21 .98 RPM
SRP051959_kidney 0 .00 RPM 12 .38 RPM
SRP051959_liver 0 .00 RPM 14 .66 RPM
SRP051959_lung 0 .00 RPM 26 .00 RPM
SRP051959_lymph_node 0 .00 RPM 32 .99 RPM
SRP051959_skeletal_muscle 0 .00 RPM 15 .46 RPM
SRP051959_spleen 0 .00 RPM 23 .61 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_3707 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_3707 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3707 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000053841 retrocopy
Canis familiaris ENSCAFG000000136861 retrocopy
Callithrix jacchus ENSCJAG000000072613 retrocopies
Callithrix jacchus ENSCJAG000000076301 retrocopy
Callithrix jacchus ENSCJAG00000013392 7 retrocopies
Callithrix jacchus ENSCJAG000000365171 retrocopy
Dasypus novemcinctus ENSDNOG000000078095 retrocopies
Equus caballus ENSECAG000000164341 retrocopy
Erinaceus europaeus ENSEEUG000000104462 retrocopies
Echinops telfairi ENSETEG000000168932 retrocopies
Homo sapiens ENSG000001164731 retrocopy
Myotis lucifugus ENSMLUG000000105713 retrocopies
Monodelphis domestica ENSMODG000000013233 retrocopies
Mus musculus ENSMUSG000000687982 retrocopies
Nomascus leucogenys ENSNLEG000000040181 retrocopy
Ochotona princeps ENSOPRG000000039993 retrocopies
Pongo abelii ENSPPYG000000010281 retrocopy
Pan troglodytes ENSPTRG000000011021 retrocopy
Rattus norvegicus ENSRNOG000000324633 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000278471 retrocopy
Tarsius syrichta ENSTSYG000000045213 retrocopies
Vicugna pacos ENSVPAG000000100331 retrocopy



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