RetrogeneDB ID:

retro_cjac_2203

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:3:177173465..177175800(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HDAC6
Ensembl ID:ENSCJAG00000002395
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2203
AGCCTAGAATATATTGATCTGATGGAAACAACACAGTACATGAATGAGGGAGAACTGCACGTCCTAGCAGACACCTGTGA
CCCAGTTTATTTTCATCTGAACTCATACTCATGTGCCTGCCTGGCCTCAGCCTCTGTCCTCAGGCTGGTGGATGTGGTCC
TGGGGGCTGGAATCTGGAATGGCATGGCATCATTAGGCTTCCTGCACATCATGCCCAGCACAGTTTTATGGATGGCTGTT
GCATATTCAGTCACATGGTTGTGGCAGCCTGCTATGCTCAATAGAAACACCACATCCGGAGGGTCTTTGTGGTGGATTGG
GATGTGCACCACAGTCAAAAGCACAGTTCACCTTCAACCAGGACCCCTGTGTCCTCTATTTCTTCATCCACCACTATGAG
CAGGGTAGGTTCTGGCCCCACCTGAAGGCCTCTAACTGGTCCACCACAGGTTTTGGTCAAGGCCAAGGATATACCATCAA
TATTCCTTGGAACCAGGTGGGTATGAGAGATGCTGACTATATTGCTGCTTTCCTTCACGTCCTGCTGCTGGTCATCCTTG
AGTTCCAGCCTCAGCTGGTCCTGGTGGCTACTGGATTTGATACCCTGCAAGGGACCCCAAGGGTGAGATGGCTGCCACTC
CAGCAGGGTTCACCCAGCTAACCCACCTGCTCATGGGTCTGGCAGGAGGCAAGCTGACTCTGTTTTTGGAGGGTGGCTAC
AACCTCTGCACCCTGGCTGAAGGCATCAGTGCTTCACTCTACACCCTTCTGGGAGACCCTTGCCCTATACTGGAGTCCTC
TGGTGCCCGCTGCCAGAGTGCCCAGGCTTCAGTCTCCTGTGCTCTGGAAGCCCTTGAGCCCTTCTGAGAGGTTCTTGTGA
GATCAACTGAGACCAGGGAGGGGGACAACATGGAGGAGGACAATGTAGAAGAGAGAGAGGAGGAAGGACCTGGGAGCCCT
TGCTCCCAATCCTGACATGACCGGTGCTACAGTCTCACACAGGACTGGTCTCTGACAAAAGTATGATGAATCACTGCAAC
TTGTGGGACAGCCACCACCCCAAGGTACCCCAGGGCATCATGTGGATCATGTGCCGTCTGGAGGAGCTGGGGCTTGCTGG
GGGCTGCCTCACTCTGCCACGGCGCCCCTCCACAGACGCCGAGCTGTTCACCTGCCACAGTGCTGAGTACGTGGTGCATC
TCCAGGCCACAGAGAAGATGAAAACCCAGGAGCTGCACCGTGACAGCTTTGACTCTATCTACATCTGCCCCAGCACCTTC
GCCTGTGCACAGCTTGCCACTGGCACTGCCTGCTGCCTGGTGGAGGCCATGCTCTCAGGAGAAGTTCCGAATGGTGCTGC
AGTGGCATGTACCTCAGGACACCATGCGGAGCAGGACACAGCTTGTGGTTTTGCTTTTTAAACTCCGTGGCTGTGGCTGC
ATTCCATGCCCAGGCTATCAGTGGGTGTGTCCTGCGGATCCTGATCATGGATTGGGATGTTCACCATAGTAATGGAACTC
AGCACATGTTTGAGGATGACCCCAGTGTGCTATATGTGTCCCTGCACCGCTATGACACTGGCAACTTCTTCCCCATGGGA
GATGAGGGTGCCAGCAGCCAGATCAGCCAAGCTGCAGGCACAAGCTTCACCACCAATGTGGCATGGAATGGGCCCCTCAT
AGTTGATGCTGACTGCCTAGCTGCCTGGCATCACCTGGTGCTTCCCACTGCCTGCAAGTTTAACCCAGAACTGGTGTTGG
TTTCAGCTGGCTTTGACACTGCACGGGGGGACCTGCAGGGGAGCTTCCAGGTGTTATCTGAGGTTTACGCCCACCTCACC
TACCTGCTGATAGGTCTTGTCAGTGGCAGCATTATTCTTATCCTAGAGGGTGGCTATATGCTGACGTCCATCTCAGAGTC
CATGGCTGCCTGCACTTGCTCCCTCCTTGAAGACCAGCCAACCGTCCTGACCCTGCCAGGGCCCCCACTATCAGGGTCCC
TGGCCTCAATCACTGAGACCATCCAAGTCCATCATAGATACTGGCCCAGCTTACGGGTCATGAAGGTAAAAGATAAAGAG
GGATTCTCCAGTTCTGAGTTGGTCACCAAGAAGGCACCCCACCCAGCCAAACCTAGGTTAGCTGAGTGAATGACAACATG
AGAAAAGAAGGTTCTGGAAGCAGGCATGGGGAAGGTCATCTCAGCATCATCTGGGGAAGAGTCCACTCTGGGTCGGACTA
AGTCAGAGACAGCTGTAGTGGCACTCACTGAGGACCAGTCCTCAGAGGCAGCCACTGGGGGAGCCATGCTGGCCCAGACC
ATCTCCAAGGCAGCC

ORF - retro_cjac_2203 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 80.2 %
Parental protein coverage: 63.73 %
Number of stop codons detected: 5
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalSLEYIDLMETTQYMKEGELRVLADTYDSVYLHPNSYSCACLATGSVLRLVDAVLGAEIRNGMA-IIRPPG
SLEYIDLMETTQYM.EGEL.VLADT.D.VY.H.NSYSCACLA..SVLRLVD.VLGA.I.NGMA.IIR.P.
RetrocopySLEYIDLMETTQYMNEGELHVLADTCDPVYFHLNSYSCACLASASVLRLVDVVLGAGIWNGMA<IIRLPA
ParentalHHAQHSLMDGYCMFNHVAVAARYAQQKHRIQRVLIVDWDVHHGQG-TQFTFDQDPSVLYFSIHRYEQGRF
HHAQHS.MDG.C.F.H..VAA.YAQ.KH.I.RV..VDWDVHH.Q...QFTF.QDP.VLYF.IH.YEQGRF
RetrocopyHHAQHSFMDGCCIFSHMVVAACYAQ*KHHIRRVFVVDWDVHHSQK<AQFTFNQDPCVLYFFIHHYEQGRF
ParentalWPHLKASNWSTIGFGQGQGYTINVPWNQVGMRDADYIAAFLHVLLPVTLEFQPQLVVVAAGFDALQG-DP
WPHLKASNWST.GFGQGQGYTIN.PWNQVGMRDADYIAAFLHVLL.V.LEFQPQLV.VA.GFD.LQG.DP
RetrocopyWPHLKASNWSTTGFGQGQGYTINIPWNQVGMRDADYIAAFLHVLLLVILEFQPQLVLVATGFDTLQG<DP
ParentalKGEMAATPAGFAQLTHLLMGLAGGKLILSLEGGYNLRALAEGVSASLHTLLGDPCPMLESPGAPCRSAQA
KGEMAATPAGF.QLTHLLMGLAGGKL.L.LEGGYNL..LAEG.SASL.TLLGDPCP.LES.GA.C.SAQA
RetrocopyKGEMAATPAGFTQLTHLLMGLAGGKLTLFLEGGYNLCTLAEGISASLYTLLGDPCPILESSGARCQSAQA
ParentalSVSCALEALEPFWEVLVRSTDTVEGDNVEEDNIEESEDERP-WEPPVLPILTWPVLQSRTGLVYDQSMMN
SVSCALEALEPF.EVLVRST.T.EGDN.EEDN.EE.E.E.P.WEP..LPILT.PVLQS.TGLV.D.SMMN
RetrocopySVSCALEALEPF*EVLVRSTETREGDNMEEDNVEEREEEGP<WEP-LLPILT*PVLQSHTGLVSDKSMMN
ParentalHCNLWDSHHPEVPQRILRIMCRLEELGLAGRCLTLPPRPATEAELFTCHSAEYVARLRATEKMKTRELHR
HCNLWDSHHP.VPQ.I..IMCRLEELGLAG.CLTLP.RP.T.AELFTCHSAEYV..L.ATEKMKT.ELHR
RetrocopyHCNLWDSHHPKVPQGIMWIMCRLEELGLAGGCLTLPRRPSTDAELFTCHSAEYVVHLQATEKMKTQELHR
ParentalESSNFDSIYICPSTFACAQLATGAACRLVEAVLSGEVLNGAAVVRPPGHHAEQDAACGF-CFFNSVAVAA
.S..FDSIYICPSTFACAQLATG.AC.LVEA.LSGEV.NGAAV....GHHAEQD.ACGF.CF.NSVAVAA
RetrocopyDS--FDSIYICPSTFACAQLATGTACCLVEAMLSGEVPNGAAVACTSGHHAEQDTACGF<CFLNSVAVAA
ParentalRHAQAISGHALRILIVDWDVHHGNGTQHMFEDDPSVLYVSLHRYDHGTFFPMGDEGASSQIGRAAGTGFT
.HAQAISG..LRILI.DWDVHH.NGTQHMFEDDPSVLYVSLHRYD.G.FFPMGDEGASSQI..AAGT.FT
RetrocopyFHAQAISGCVLRILIMDWDVHHSNGTQHMFEDDPSVLYVSLHRYDTGNFFPMGDEGASSQISQAAGTSFT
ParentalVNVAWNGPRIGDADYLAAWHRLVLPIAYEFNPELVLVSAGFDAARGDPLGGCQISPEGYAHLTHLLMGLA
.NVAWNGP.I.DAD.LAAWH.LVLP.A..FNPELVLVSAGFD.ARGD..G..Q...E.YAHLT.LL.GL.
RetrocopyTNVAWNGPLIVDADCLAAWHHLVLPTACKFNPELVLVSAGFDTARGDLQGSFQVLSEVYAHLTYLLIGLV
ParentalSGRIILILEGGYNLTSISESMAACTRSLLGDPPPLLTLPRPPLSGALASITETIQVHRRYWRSLRVMKVE
SG.IILILEGGY.LTSISESMAACT.SLL.D.P..LTLP.PPLSG.LASITETIQVH.RYW.SLRVMKV.
RetrocopySGSIILILEGGYMLTSISESMAACTCSLLEDQPTVLTLPGPPLSGSLASITETIQVHHRYWPSLRVMKVK
ParentalDKEGPSSSKLITKKAPQPAKPMLAERMITREKKVLEASMGKVISV-SGEESTPDQVKSETAVVAVTQDQS
DKEG.SSS.L.TKKAP.PAKP.LAE.M.T.EKKVLEA.MGKVIS..SGEEST....KSETAVVA.T.DQS
RetrocopyDKEGFSSSELVTKKAPHPAKPRLAE*MTT*EKKVLEAGMGKVISASSGEESTLGRTKSETAVVALTEDQS
ParentalSKAATGGATLAQTVSKAA
S.AATGGA.LAQT.SKAA
RetrocopySEAATGGAMLAQTISKAA

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 11 .94 RPM
SRP051959_heart 0 .00 RPM 19 .87 RPM
SRP051959_kidney 0 .00 RPM 34 .19 RPM
SRP051959_liver 0 .00 RPM 25 .34 RPM
SRP051959_lung 0 .02 RPM 22 .01 RPM
SRP051959_lymph_node 0 .00 RPM 19 .59 RPM
SRP051959_skeletal_muscle 0 .00 RPM 13 .30 RPM
SRP051959_spleen 0 .00 RPM 20 .46 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_2203 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2203 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2203 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 ENSCJAG00000002395 1 retrocopy
retro_cjac_2203 ,


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