RetrogeneDB ID:

retro_cjac_4186

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:69359402..69360635(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC52A3
Ensembl ID:ENSCJAG00000020873
Aliases:None
Description:solute carrier family 52 (riboflavin transporter), member 3 [Source:HGNC Symbol;Acc:16187]


Retrocopy-Parental alignment summary:






>retro_cjac_4186
GCCTTCCTGATGCACCTGCTGGTCTGCATCTTTGGAATGGGCTCCTGGGTGACCATCAATGGGCTCTGGGTAGAGCTGCC
CTTGCTGGTGATGGAGCTGCCCGAGAGCTAGTACCTGCCCTCCTACCTCACAGTGGTCATCCAGCTGGCCAACATTGGGC
CCCTCCTGGTCACCCTGCTCCATCACTTCCGGCCCAGCTGCCTTTACAAAGTGCCCATCATCTTTACCCTGCTGGGCATG
GAAACTGTCACCTGAATCATCTTTGCCTTCCTCTGGAATATGACCTCCTGGGTGCTAGACAGCCACCACAGAATCGCCTT
CTTGGTCCTCACCTTCTTCCTCGCCCTGGTGGACTGCGCCTCTTCGGTCACCTTCCTCCCCTTCATGAGCCAGCTGCCCA
CCTAATATCTGACTTCCTTCTTTGTGGGTAAAAGACTCAGTGGCCTCTTGCCTGCCCTGGTGGCTCATGCCAGAGCTCGG
GTCTCACCATCTGCATCAATGTCACTGAGATGTCAGACAGCATACCAAGCCCTGTGCCCACAGGGGAGATTGACATCGCA
CAGGGAGTTTCCAGAGCCTTGGAGTCTGCCCTCCCCAGAACAGCAGCACCCCATCCCACCTGGGGAGCCGCTACCTCCCC
ACCCACTTCTCACCCCTGGTCTTCTTCCTCCTACTGTCCTTCATGATGGCCTGCTGCCTCGTGGCATTCTTTGTCCTCCA
GCATCAACCCTGGTGCTGGGAGGCCTCCATGGAAGACCTCCTCAACAACCAGGTCACCTCCCATTCCATCCGGCCGCAGG
AAGAGAATGACTTGGTCCCTTCAGGCACAATGGACAGCAGCCAGGGCCAGAGGCATCTAGATGAGAAAGCAGCCCCCTGC
TGCCCAGCCCACCTGACCTTTATCTATACCCTGGTGGTCTTTGTCCATGCACTCACCAACAGCATGCTGCCCTCTGTCTA
AACCTACTCCTGCCTGTCCTATGGGCCGGTTGCCTACCACCTGGCCACCATCCTCAGCATTGTGGCCAACACTCTTGCCT
CCTTGCTCTCCATGTTCCTGCCTAACAGGTCTCTGCTGTTCCTGGGGGTCCTCTCCGAGCTCAAGACCTGCTTTGGGGGC
TACAACATGGCCATGGCGGTGATGAGCCCCCTGCCCACCTCCTGCAGGGCCACTGGGGTGGGGAAGTCCTCATCGTGGCC
TCATGGGTGCTGTTTAGCGGCTGTCTTAGCTAC

ORF - retro_cjac_4186 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.3 %
Parental protein coverage: 87.63 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalAFLIHLLVCIFGMGSWVTINGLWVELPLLVMELPEGWYLPSYLTVVIQLANIGPLLVTLLHRFRPSCLSE
AFL.HLLVCIFGMGSWVTINGLWVELPLLVMELPE..YLPSYLTVVIQLANIGPLLVTLLH.FRPSCL..
RetrocopyAFLMHLLVCIFGMGSWVTINGLWVELPLLVMELPES*YLPSYLTVVIQLANIGPLLVTLLHHFRPSCLYK
ParentalVPIIFTLLGMGTVTCIIFAFLWNMSSWVLDRHHSIAFLVLTFFLALVDCTSSVTFLPFMSRLPTYYLTTF
VPIIFTLLGM.TVT.IIFAFLWNM.SWVLD.HH.IAFLVLTFFLALVDC.SSVTFLPFMS.LPT.YLT.F
RetrocopyVPIIFTLLGMETVT*IIFAFLWNMTSWVLDSHHRIAFLVLTFFLALVDCASSVTFLPFMSQLPT*YLTSF
ParentalFVGEGLSGLLPALVALA-QGSGLTTCVNVTEMSDSMPSPVPTGETDITQGIPTALVSTLPRTAAPL-SHL
FVG..LSGLLPALVA.A.Q.SGLT.C.NVTEMSDS.PSPVPTGE.DI.QG...AL.S.LPRTAAP..SHL
RetrocopyFVGKRLSGLLPALVAHA<QSSGLTICINVTEMSDSIPSPVPTGEIDIAQGVSRALESALPRTAAPH<SHL
ParentalETRYLPAHFSPLVFFLLLSFMMACCLMAFFVLQRQPRCWEASVEDLLNDQVTLHSIRPREENDLGPTGTV
..RYLP.HFSPLVFFLLLSFMMACCL.AFFVLQ.QP.CWEAS.EDLLN.QVT.HSIRP.EENDL.P.GT.
RetrocopyGSRYLPTHFSPLVFFLLLSFMMACCLVAFFVLQHQPWCWEASMEDLLNNQVTSHSIRPQEENDLVPSGTM
ParentalDSSQGQGHLEEKAAPCCPAHLAFIYTLVAFVNALTNGVLPSVQTYSCLSYGPVAYHLAATLSIVANPLAS
DSSQGQ.HL.EKAAPCCPAHL.FIYTLV.FV.ALTN..LPSV.TYSCLSYGPVAYHLA..LSIVAN.LAS
RetrocopyDSSQGQRHLDEKAAPCCPAHLTFIYTLVVFVHALTNSMLPSV*TYSCLSYGPVAYHLATILSIVANTLAS
ParentalLLSMFLPNRSLLFLGFLSGLGTCFGGYNMAMAVMS-PCP-LLQGHWGGEVLIVASWVLFSGCLSY
LLSMFLPNRSLLFLG.LS.L.TCFGGYNMAMAVMS.PCP.LLQGHWGGEVLIVASWVLFSGCLSY
RetrocopyLLSMFLPNRSLLFLGVLSELKTCFGGYNMAMAVMS>PCP>LLQGHWGGEVLIVASWVLFSGCLSY

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






RNA-Seq - click to see more details

(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 .04 RPM 1 .58 RPM
SRP051959_heart 0 .19 RPM 1 .07 RPM
SRP051959_kidney 0 .11 RPM 0 .55 RPM
SRP051959_liver 0 .22 RPM 0 .04 RPM
SRP051959_lung 0 .15 RPM 0 .02 RPM
SRP051959_lymph_node 0 .07 RPM 0 .00 RPM
SRP051959_skeletal_muscle 0 .13 RPM 0 .07 RPM
SRP051959_spleen 0 .02 RPM 0 .00 RPM

ChIP-Seq - click to see more details

Callithrix jacchus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cjac_4186 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4186 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4186 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000020873 1 retrocopy
retro_cjac_4186 ,


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