RetrogeneDB ID:

retro_cjac_2229

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:33583781..33585267(-)
Located in intron of:ENSCJAG00000001492
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:KANSL3
Ensembl ID:ENSCJAG00000007688
Aliases:None
Description:KAT8 regulatory NSL complex subunit 3 [Source:HGNC Symbol;Acc:25473]


Retrocopy-Parental alignment summary:






>retro_cjac_2229
GAATCAGACATCCCAATAGATGGGAGACGGTTATGTCAACCCCTGTGCCACTCTATGACAATCAGAAGGCATGCAGCATG
ATGAATGCGTGTGAACGGCATGTCATCTTCTCCAGAACTGATGCAGATGCCCCTCCTCCACCAGAGACTGTGAGGAGTAC
GTCAACAGGACTGGCTGGACAATGGCCCAGAGCAAGCTATTCAACAAGATCCTCAAAGCCCTGCAGTCTGACCAGCTTGC
CCACTTGGCCAGTGAAGGGGCTTGTAATGAGCCAGTGCTGCACCGTGTTGCTGTGGACAAGTGTGTGAGGAGAGTGCAGC
CAGCTCTGGCAAGTGTGAGCTGGGACACCAAGCTTATCCAATGGCTGCACACCACCCTTATGGAGACCTTGAGTCTGCCC
ATGCTGGCAGCCTACCTGGATGCTTTGCAGATGCTGAAGGGGAAGATCCCAACCTTGATTGACCGGATGCTTCTGTCATC
CAACACGAAGGCTGGGGCTGCAGGAGCTGAAGCCTTGTCTCTCCTACTGAAGAGGACCTGGGACCCTGCTGTGGAGGCGC
GTTCTCATTACAAACCAAGCAAACTCCCTGGCACCCCATTGATTCTCATCACTTTCTCTGGTCCCTCCAGCTCTGTGATT
CCCACTTCATGCCACCACCGATTCTGGCACTCTCAGCTCTCCTGCTCAGGCAAGGTCATCCCTGTAGCCACCCATCTGCT
GAACAATGGCAGTGGGGTAAGAGTTTTGCAGTGTCTCGAGCATATTATTGGGGCGGTGAGAAGCAAAGTGCTGGAGATTC
ACAGCCATTTCCCACACAAACCCATTATCTTGATTGGCTGGAACACAGGAGCTTTGGTGGCCTGTCATGTGTCAGTGATG
GAGTGTGTCACTGCAGTTGTCTGCCTTGGGTTTCCTCTATTTATTGTGGATGGCCCAAGAGGGGATATAGATGATCCCCT
CCTGGATATGAAGACTCCAGTCCTCTTTGTCGTTGTTCAGAATTCCCTTCAGTGTCACCCTGAAGCCATGGAGGGCTTCG
GGGAGAGGATTTGAGCTGAGAGCAGCTTGGTAGTGTTTGGGGGAGCTGATGAGAATCTCAGAATAAGCAAAGCAAGGAAA
AAATCAGAAGAATTGACTCAGAGCATGGTGGACAGATGTATTCAGGAAGAGATTGTGGACTTTCTGACTGGAGTGCTCAC
TCGTGCTGAGGGTCATCTGGGCTCTGAACCTCAGGGTCAGGATGCGGAGAAGAAGCCCCACGACGTAGCCTGCAGAGACT
TGGCCTTTGAAGTCCCTGAGAGGGGCAGTCAACCTGCTTCCCCAGCTGCCAAGCTGCCCGACTTGCCCTCAGGAGAGGAT
CTCTCCAGTGTGTCCAGCAGCCTCACCTCCAGTCTCAAGACCAAAGTGACCACAGTGACCTCTGCCCTGAAGTCCGGTCA
GATTGGAAGCTCTCAGCTGCTGAAGAGACATGTGCAGCGAGCGGAC

ORF - retro_cjac_2229 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.03 %
Parental protein coverage: 55.2 %
Number of stop codons detected: 1
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalESDIPIDV-ETVTSTPVPLYDNQKARSVMNECERHVIFARTDADAPPPPE-DWEEHVNRTGWTMAQNKLF
ESDIPID..ETV.STPVPLYDNQKA.S.MN.CERHVIF.RTDADAPPPPE.D.EE.VNRTGWTMAQ.KLF
RetrocopyESDIPIDG<ETVMSTPVPLYDNQKACSMMNACERHVIFSRTDADAPPPPE<DCEEYVNRTGWTMAQSKLF
ParentalNKILKALQSDRLARLANEGACNEPVLRRVAVDKCARRVRQALASVSWDTKLIQWLHTTLVETLSLPMLAA
NKILKALQSD.LA.LA.EGACNEPVL.RVAVDKC.RRV..ALASVSWDTKLIQWLHTTL.ETLSLPMLAA
RetrocopyNKILKALQSDQLAHLASEGACNEPVLHRVAVDKCVRRVQPALASVSWDTKLIQWLHTTLMETLSLPMLAA
ParentalYLDALQTLKGKIPTLIDRMLVSSNTKTGAAGAEALSLLLKRPWDPAVGVLSHNKPSKLPGSPLILIASSG
YLDALQ.LKGKIPTLIDRML.SSNTK.GAAGAEALSLLLKR.WDPAV...SH.KPSKLPG.PLILI..SG
RetrocopyYLDALQMLKGKIPTLIDRMLLSSNTKAGAAGAEALSLLLKRTWDPAVEARSHYKPSKLPGTPLILITFSG
ParentalPSSSVFPTSRRHRFWQSQLSCLGKVIPVATHLLNNGSGVGVLQCLEHMIGAVRSKVLEIHSHFPHKPIIL
PSSSV.PTS..HRFW.SQLSC.GKVIPVATHLLNNGSGV.VLQCLEH.IGAVRSKVLEIHSHFPHKPIIL
RetrocopyPSSSVIPTSCHHRFWHSQLSCSGKVIPVATHLLNNGSGVRVLQCLEHIIGAVRSKVLEIHSHFPHKPIIL
ParentalIGWNTGALVACHVSVMEYVTAVVCLGFPLFTVDGPRGDVDDPLLDMKTPVLFVIGQNSLQCHPEAMEDFR
IGWNTGALVACHVSVME.VTAVVCLGFPLF.VDGPRGD.DDPLLDMKTPVLFV..QNSLQCHPEAME.F.
RetrocopyIGWNTGALVACHVSVMECVTAVVCLGFPLFIVDGPRGDIDDPLLDMKTPVLFVVVQNSLQCHPEAMEGFG
ParentalEKIRAENSLVVVGGADDNLRISKAKKKSEGLTQSMVDRCIQDEIVDFLTGVLTRAEGHMGSEPRDQDAEK
E.I.AE.SLVV.GGAD.NLRISKA.KKSE.LTQSMVDRCIQ.EIVDFLTGVLTRAEGH.GSEP..QDAE.
RetrocopyERI*AESSLVVFGGADENLRISKARKKSEELTQSMVDRCIQEEIVDFLTGVLTRAEGHLGSEPQGQDAE-
ParentalKKKPRDVARRDLAFEVPERGSRPASPATKLPASPSGSEDLSSVSSSPTSSPKTKVTTVTSAQKSSQIGSS
.KKP.DVA.RDLAFEVPERGS.PASPA.KLP..PSG.EDLSSVSSS.TSS.KTKVTTVTSA.KS.QIGSS
Retrocopy-KKPHDVACRDLAFEVPERGSQPASPAAKLPDLPSG-EDLSSVSSSLTSSLKTKVTTVTSALKSGQIGSS
ParentalQLLKRHVQRTE
QLLKRHVQR..
RetrocopyQLLKRHVQRAD

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 .00 RPM 28 .98 RPM
SRP051959_heart 0 .05 RPM 38 .29 RPM
SRP051959_kidney 0 .00 RPM 44 .51 RPM
SRP051959_liver 0 .04 RPM 21 .57 RPM
SRP051959_lung 0 .24 RPM 39 .11 RPM
SRP051959_lymph_node 0 .00 RPM 44 .40 RPM
SRP051959_skeletal_muscle 0 .00 RPM 22 .93 RPM
SRP051959_spleen 0 .00 RPM 41 .83 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_2229 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2229 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2229 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 ENSCJAG00000007688 1 retrocopy
retro_cjac_2229 ,


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