RetrogeneDB ID:

retro_cjac_981

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:12:53235001..53235867(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000014769
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSCJAG00000017209
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_981
GGCCCAAGCCACAGCAGCTTCCCAGTGGGATGCCGCCACCCCACCGTGCTGCGCATGGTGCTGGATGTGCTGCAGGCAGG
GGAGCAGTGTCGGGGCACATCGGTGGCAGCCATCAAGCTCTACATCTTGCAAAAGTACCCAGCGGTGGATGTCCTTCGCT
TCAAGTACCTGCTGAAGAAGGCGCTGGCCATTGGCATGTGCCGTGGCCTCCTCGCCAGGCCCCTCAACTCCAAAGCCAGC
GGGGCCACTGGCAGCTTCAAATTAGTTACCAAGTACAAGAGGAAAATCAAGCCCAGGAAGATGGCTTCCCCGAAGGCCCC
CAGGAGAGCAGGCGAGGCCAAGGGGAAGTCTTTAAGAAACCAGATGAGGCCAAGGAGGAGGCTTCCAAGGCAGGCAAGGT
GAAAAAGGCAGCCAAGAGGCCAACAGAGGTGCAGAAGTTTCCTCTCAAGACAGGCACAGCCACAGAAAAAGCTCACAAAC
AAGGCAGCAAGGCCAAGGACACCAAGGCACAGCCAGGCGAAGCTCAGAAGGTGCCCCCCAAGCCAGACAAGGCCATGCAG
GCCTCTTCTAATGTCAGCAGGTTCAGCAGGAAGGCAGAGGCCAAAGGAAGCAGGAGGAGCCAAGGAGATGCTGAGGCCTG
CAGGAACACCAAAACCGGGAGTAGGAGTTCAAGACCTACGGTCAGCAAGGTCAAGAATGGTGCTGCTTCCCCAACCAAAA
AGAAGTTGGTGGCCAAGGCCAAGGCCCAGGCCCCTAGAGGGGCAGCTGCCCCTGGGGCTGGGCAGGGGCTGAATGCCAAG
GGTGCTTCTGCTAAGGCCAATGGGTCCAAGGTGGTGCCTGCACACTTGTCCAGGAAGACAGAGGCC

ORF - retro_cjac_981 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 74.06 %
Parental protein coverage: 91.51 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalGPSRSSFPVGRRHPPTLQMVLEAMQVLQAEEQRQGTSVVAIKRYILRKYPAADGPRFKYLLKNALATGMC
GPS.SSFPVG.RHP..L.MVL....VLQA.EQ..GTSV.AIK.YIL.KYPA.D..RFKYLLK.ALA.GMC
RetrocopyGPSHSSFPVGCRHPTVLRMVLD---VLQAGEQCRGTSVAAIKLYILQKYPAVDVLRFKYLLKKALAIGMC
ParentalRGLLARPPHLKTRGATGSFQLVTNHERTIKPRKTASPKAPRRAGVAKGK-VPKKPDEAKEEPPKAGKGKK
RGLLARP...K..GATGSF.LVT...R.IKPRK.ASPKAPRRAG.AKGK.V.KKPDEAKEE..KAGK.KK
RetrocopyRGLLARPLNSKASGATGSFKLVTKYKRKIKPRKMASPKAPRRAGEAKGK<VFKKPDEAKEEASKAGKVKK
ParentalGAKSPAEVQKPPLKPGTDTEKACKESSKAKDTEAQPGEAQKVPPKPDKAMRAPSNDSGFSRRAEVKGSWR
.AK.P.EVQK.PLK.GT.TEKA.K..SKAKDT.AQPGEAQKVPPKPDKAM.A.SN.S.FSR.AE.KGS.R
RetrocopyAAKRPTEVQKFPLKTGTATEKAHKQGSKAKDTKAQPGEAQKVPPKPDKAMQASSNVSRFSRKAEAKGSRR
ParentalSPGGAEASRKTKAGSKSLRPTVSKVKSGTASLTEKKSVARAKAQS-QAPAPTGAGQGPNAKGASAKAGGS
S.G.AEA.R.TK.GS.S.RPTVSKVK.G.AS.T.KK.VA.AKAQ.....A..GAGQG.NAKGASAKA.GS
RetrocopySQGDAEACRNTKTGSRSSRPTVSKVKNGAASPTKKKLVAKAKAQAPRGAAAPGAGQGLNAKGASAKANGS
ParentalKVVPAHLSRKTEA
KVVPAHLSRKTEA
RetrocopyKVVPAHLSRKTEA

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 0 .00 RPM
SRP051959_heart 0 .00 RPM 0 .00 RPM
SRP051959_kidney 0 .00 RPM 0 .00 RPM
SRP051959_liver 0 .00 RPM 0 .00 RPM
SRP051959_lung 0 .00 RPM 0 .00 RPM
SRP051959_lymph_node 0 .02 RPM 0 .02 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .00 RPM
SRP051959_spleen 0 .00 RPM 0 .02 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_981 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_981 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_981 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 11 parental genes, and 15 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000017209 2 retrocopies
retro_cjac_3976, retro_cjac_981 ,
Felis catus ENSFCAG000000000942 retrocopies
Homo sapiens ENSG000001788041 retrocopy
Gorilla gorilla ENSGGOG000000007351 retrocopy
Myotis lucifugus ENSMLUG000000252262 retrocopies
Oryctolagus cuniculus ENSOCUG000000293791 retrocopy
Ochotona princeps ENSOPRG000000103712 retrocopies
Pongo abelii ENSPPYG000000134141 retrocopy
Pan troglodytes ENSPTRG000000153801 retrocopy
Pteropus vampyrus ENSPVAG000000071101 retrocopy
Tursiops truncatus ENSTTRG000000112761 retrocopy



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