RetrogeneDB ID:

retro_cjac_3858

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL285215.1:14139..15897(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NOD2
Ensembl ID:ENSCJAG00000001786
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3858
CAGTCCCCGTTCCTCAGGAAGTCAGGAAGGGGCAGAGACGCTTTGCCTGGAGGACATATACCCAGAGAATGTCCTGGAGG
TCTGGGCAGATATGGGCATGGCTGGATCCCTGCAGAAGAGCCCGGACACCCTGGGGCTGGAGGAGCTCTTCAGCACCCTT
GGCCACCTCAGTGAAGATGTGCTGGTGGGGGGTGAGGCAGGCAGTGGCAAGAGCATGCTCCTGCAGCGTCTGCACTTGCC
GTGGGCTGCAGGGCGAGACTTCCAGGAATTTTTCTTTGTCTTCCCATTCAGCTGCCGGCAGCTGCAGTGAATGGTTAAAC
CACTCTCTGTGCGGATGCTACTCTTTGAGCACTGCTGTTGGCCTGACCTTGATCAACAGGACATCTTCCAGTTTCTCCTT
GACCACCCTGACCGTGTCCGGCTAACCTTTGATGGCTTTGATGAGTTCAAGTTCAGGTTCACGGATTGCGAATGTCACTG
CTCCCTGACAGACCCCACCTCTGTCCAGACTCTGCTCTTTAACCTTCTGCAGGTCAACCTGCTGAAGAATGCCCGCAAGG
TGGTGACCAGCCGTCCTGCTTCCGTGTCGGCGTTCCTCAGGAAGTACATCTGCACCGAGTTCATCCTCAAGGGCTTCTCC
GAAGAGGGCATCGAGCTGTACTTGAGGAAGCGCCATCATGATCCTGGAGTGGCAGACCGCCTCATTCGCCTGCTCCAAGC
GTCCTCAGCCCTGAGTGGTTTGTGCCACCTTCCTGTGTTCTCATGGATGGTGTCCAAATGCCACCAGGAACTGTTGCTGC
AGAGGGCGGGGGGGATCCCCAAAGACCACTACAGATATGTACCTGCTGATCCTGCAGCATTTTCTGCTGCATGCCATCCC
CCCAGACTCAGCCTGCCAGGGTCTAGGACCCAGTCTCCTTCTGGGCCACCTCCCCACCCTCCTGTGCCTCGGCAGACTTG
CTCTCTGGGCCTGGGCATGTGCTGCTATGTGTTCTCAGCCCAGCAGCTCCAGGCAGCACAGGTCAGTCCTGATGACATTT
CTCTTGGCTTCCTGGTATGTGCCAAAGGTGTCATGCCAGAGAGTACAGTGCCCCTGGAATTCCTGCACATCACTTTCCAG
TGCTTCTTTGCCGTGTTCTACCTGGCACTCAGTGCTGATGTGCCGCCAGCCTTGATCAGGCACCTCTTCAGTTGTGGCAG
GCCAGGCAACTCGCTGATGGCCAGGCTCCTGCCCATGCTGTGCATCCAGGGCTTGCAGGGGAAGGACGGCAGTGTGGCAG
CTTTGCTGCAGAAGACTGAGCTGCACAGCCTTTAGATCACAGCAGCCTTCCTGGCAGGGCTGTTGTCCTGAGAGCACTGG
GGCCTGCTGGCCGAGTGCCAGGCATCCGAGAAGGCCCTGCTCCGGCGCCAGGTCTGTGCCCGCTAGTGTCTGGCCCGCAG
CCTCTGTAAGCACTTCCACTCCATCCTGCCAGCCGTGCCAGGTGAGGCCAAGAGCATGCACGCCATGTCCAGGTTCATCT
GGCTCATACAGAGCCTGTACGAGATGCAAATGAGCAGCTGGCATGGAAGGCTGTACGTGGCCTGAATGTCGGGCACCTCA
AGTTGACATTTTGCAGCATGGGCCCCACTGAGTGTGCTGCCCTGGCCTTCGTGTGGTGGCACCTCCAGCAGCCCGTGGCC
CTGCAGTTGGACTACAACTCTGTGGGTGACATTGATGTGGAGCAGCTTCTGCCTTGCCTTGGTGTCTGCAAGGCTCTG

ORF - retro_cjac_3858 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.38 %
Parental protein coverage: 72.66 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalQSRFL-STYDGAETLCLEDIYTENVLEVWADVGVAGLPQKSPATLGLEELFSTPGHLSDDADTVLVVGEA
QS.FL.....GAETLCLEDIY.ENVLEVWAD.G.AG..QKSP.TLGLEELFST.GHLS.D...VLV.GEA
RetrocopyQSPFL>GSQEGAETLCLEDIYPENVLEVWADMGMAGSLQKSPDTLGLEELFSTLGHLSED---VLVGGEA
ParentalGSGKSTLLQRLHLLWAAGRDFQEFLFVFPFSCRQLQCVVKPLSVQMLLFEHCCWPDVDQQDIFQFLLDHP
GSGKS.LLQRLHL.WAAGRDFQEF.FVFPFSCRQLQ..VKPLSV.MLLFEHCCWPD.DQQDIFQFLLDHP
RetrocopyGSGKSMLLQRLHLPWAAGRDFQEFFFVFPFSCRQLQ*MVKPLSVRMLLFEHCCWPDLDQQDIFQFLLDHP
ParentalDRVLLTFDGFDEFKFRFSDRERHCSPTDPTSVQTLLFNLLQVNLLKNARKVVTSRPASMSAFLRKYIHTE
DRV.LTFDGFDEFKFRF.D.E.HCS.TDPTSVQTLLFNLLQVNLLKNARKVVTSRPAS.SAFLRKYI.TE
RetrocopyDRVRLTFDGFDEFKFRFTDCECHCSLTDPTSVQTLLFNLLQVNLLKNARKVVTSRPASVSAFLRKYICTE
ParentalFILKGFSKEGIELYLRKRHHDPGVADRLIRLLQASSALSGLCHLPVFSWMVSKCHQELMLLQR-RGGSPK
FILKGFS.EGIELYLRKRHHDPGVADRLIRLLQASSALSGLCHLPVFSWMVSKCHQEL.LLQR.RGGSPK
RetrocopyFILKGFSEEGIELYLRKRHHDPGVADRLIRLLQASSALSGLCHLPVFSWMVSKCHQEL-LLQR>RGGSPK
ParentalTTTDMYLLILQHFLLHAIPPDSACHILGPSLLLGCLPTLLRLGRLALW-GLGMCCYVFSAQQLQAAQVSP
TTTDMYLLILQHFLLHAIPPDSAC..LGPSLLLG.LPTLL.LGRLALW.GLGMCCYVFSAQQLQAAQVSP
RetrocopyTTTDMYLLILQHFLLHAIPPDSACQGLGPSLLLGHLPTLLCLGRLALW<GLGMCCYVFSAQQLQAAQVSP
ParentalDDISLGFLVCAKGVMPESTVPLEFLHITFQCFFAAFYLALSADVPPALLRHLFNCGRPGNSPMARLLPML
DDISLGFLVCAKGVMPESTVPLEFLHITFQCFFA.FYLALSADVPPAL.RHLF.CGRPGNS.MARLLPML
RetrocopyDDISLGFLVCAKGVMPESTVPLEFLHITFQCFFAVFYLALSADVPPALIRHLFSCGRPGNSLMARLLPML
ParentalCIQGSRGKDGSVAALLQKTEPHNLQITAAFLAGLLSWEHWGLLAECQASKKALLQRQACARWCLARSLRK
CIQG..GKDGSVAALLQKTE.H.L.ITAAFLAGLLS.EHWGLLAECQAS.KALL.RQ.CAR.CLARSL.K
RetrocopyCIQGLQGKDGSVAALLQKTELHSL*ITAAFLAGLLS*EHWGLLAECQASEKALLRRQVCAR*CLARSLCK
ParentalHFHSIPPAAPGEAKSMHAMPRFIWLLRSLYEMQ-DERLARKAVRGLNVGHLKLTFCSVGPTECAALAFVL
HFHSI.PA.PGEAKSMHAM.RFIWL..SLYEMQ..E.LA.KAVRGLNVGHLKLTFCS.GPTECAALAFV.
RetrocopyHFHSILPAVPGEAKSMHAMSRFIWLIQSLYEMQ<NEQLAWKAVRGLNVGHLKLTFCSMGPTECAALAFVW
ParentalRHLQRPVALQLDYNSVGDIGVEQLLPCLGVCKAL
.HLQ.PVALQLDYNSVGDI.VEQLLPCLGVCKAL
RetrocopyWHLQQPVALQLDYNSVGDIDVEQLLPCLGVCKAL

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 .13 RPM 1 .15 RPM
SRP051959_heart 0 .18 RPM 2 .32 RPM
SRP051959_kidney 0 .07 RPM 0 .98 RPM
SRP051959_liver 0 .09 RPM 2 .36 RPM
SRP051959_lung 0 .26 RPM 2 .28 RPM
SRP051959_lymph_node 0 .16 RPM 2 .03 RPM
SRP051959_skeletal_muscle 0 .59 RPM 11 .36 RPM
SRP051959_spleen 0 .08 RPM 2 .21 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_3858 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3858 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3858 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 ENSCJAG00000001786 1 retrocopy
retro_cjac_3858 ,


Copyright © RetrogeneDB 2014-2017