RetrogeneDB ID:

retro_cjac_2416

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:4:22540151..22541908(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLC4A10
Ensembl ID:ENSCJAG00000005614
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2416
CCTCAGTCCGTTCCAACTACAAGTCTTGAAGTAAAAAATGGAGTGAATTGTGAACATAGTCCTGTGGATTTAAGCAAGGT
AGACCTTCATTTCATGAAAAAAATTCCTACTGGGGCTGAGGCCTTCAATGTCCTGGTTGGAGAGGTGGATATTTTGGACC
ATCCCATTGTTGCCTTTGTGAGACTGTCTCCAGCTGTTCTTCTCTCAGGCCTAACAGAAGTTCCAATCCCAACAAGATTT
TTGTTTATCTTATTGGGTCCAGTAGGGAAAGGTCAGCAGTACCATGAGATTGGCAGATCCATGGCCACCTTCATGACAGA
TGAGATTTTTCATGACGTAGCATATAAGGCAAAAGAGCGAGATGATCTCCTGGCGGGGATTGACGAGTTCCTTGACCAGG
TGACGGTGCTCCCTCCAGGAGAGTGGGATCCCTCCATTAGAATTGAGCCACCCAAAAATGTCCCTTCCCAGGAGAAAAGG
AAAATACCTGGAGTTCCAAATGAAACTATTTGCCACATAGAACAGGAACCACATGGGGGTCACAGTGGGCCAGAACTTCA
GCTCACTGGGCGGCTATTTGGGGGCTTGGTGTTGGACATCAAGTGGAAGGCCCCCTGGTACTGGAGCGGCTACCGGGATG
CACTCAGCTTACAGTGTTTGGCCTCCTTTCTGTTCCTGTACTGTGCCTGCATGTCACCTGTCATCACCTTTGGGGGATTG
CTTGGAGAAGCCACTGAGGGACGCGTAAGTGCAATTGAATCCTTGTTTGGAGCCTCCATGACTGGGATTGCTTATTCCTT
GTTTGCGGGACAGGCTCTCACCATCCTGGGAAGTACTGGGCCAGTGCTTGTGTTTGAAAAGATTTTGTTCAAATTCTGCA
AAGACTATGCTCTTCCATACCTCTCCCTGCAAGCTTGTATTGGACTGTGGACTGCTTTCCTGTGTATTGTCCTTGTGGCA
ACTGATGCCAGTTCCCTTGTCTGCTACATTACCCGTTTCACTGAAGAAGCATTTACCTCCCCAATTTGCATTATTTTCAT
CTACGAAGCAATAGAAAAACTGATTCACCTGGCAGAGACCTATCCCATCCACATGCACAGCCAGCTGGACCACCCTAGCC
TCTATTACTGCAGGTGTACTCTCCCAGAGAATCCAAACAATCACACTCTGCAGTACTGGAAGGACCACAACATCGTGACA
GCAGAAGTCCACTGGGCTAATCTGACTGTCAGTGAATGCCAGGAGATGCATGGAGAGTTCATGGGATCTGCGTGCGGTCA
TCATGGACCCTACACTCCTGATGTCCTCTTTTGGTCCTGTATTCTCTTCTTCACCACCTTCATTCTCTCAAGCACCTTAA
AGACATTTAAGATGAGCCATTATTTCCCGACCAGAGTACGTTCCATGGTGAGTGACTTTGCTGTTTTCCTCACTATCTTC
ACAATGGTGATTATTGATTTTTTGATTGGAGTTCCACCACCAAAGCTTCAAGTTCCCAGTGTGTTCGAGCCAACAAGGGA
TGATCGAGGATGGATTATTAATCCTATTGGCCCCAATCCCTGGTGGACTGTGATAGCTGCAATTATCCCAGCTCTTCTCT
GCACTAGCTTGATATTCATGGATCAGCAGATCACAGCCGTCATTATTAATAGAAAGGAACATAAGCTCAAGAAAGGCTGT
GGCTACCACCTGGACCTACTGGTGGTGGCAATCATGCTGGGTGTCTGCTCCATCATGGGCTGCCTTGGTTTGTAGCT

ORF - retro_cjac_2416 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.71 %
Parental protein coverage: 53.77 %
Number of stop codons detected: 0
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalPQSAPAC-VENKNDVSRENSTVDFSKVDLHFMKKIPPGAEASNILVGELDFLDRTVVAFVRLSPAVLLQG
PQS.P....E.KN.V..E.S.VD.SKVDLHFMKKIP.GAEA.N.LVGE.D.LD...VAFVRLSPAVLL.G
RetrocopyPQSVPTTSLEVKNGVNCEHSPVDLSKVDLHFMKKIPTGAEAFNVLVGEVDILDHPIVAFVRLSPAVLLSG
ParentalLAEVPIPTRFLFILLGPLGKGQQYHEIGRSIATLMTDEVFHDVAYKAKDRNDLVSGIDEFLDQVTVLPPG
L.EVPIPTRFLFILLGP.GKGQQYHEIGRS.AT.MTDE.FHDVAYKAK.R.DL..GIDEFLDQVTVLPPG
RetrocopyLTEVPIPTRFLFILLGPVGKGQQYHEIGRSMATFMTDEIFHDVAYKAKERDDLLAGIDEFLDQVTVLPPG
ParentalEWDPSIRIEPPKNVPSQEKRKIPAVPNGTAAHGEAEPHGGHSGPELQRTGRIFGGLILDIKRKAPYFWSD
EWDPSIRIEPPKNVPSQEKRKIP.VPN.T..H.E.EPHGGHSGPELQ.TGR.FGGL.LDIK.KAP..WS.
RetrocopyEWDPSIRIEPPKNVPSQEKRKIPGVPNETICHIEQEPHGGHSGPELQLTGRLFGGLVLDIKWKAPWYWSG
ParentalFRDAFSLQCLASFLFLYCACMSPVITFGGLLGEATEGRISAIESLFGASMTGIAYSLFGGQPLTILGSTG
.RDA.SLQCLASFLFLYCACMSPVITFGGLLGEATEGR.SAIESLFGASMTGIAYSLF.GQ.LTILGSTG
RetrocopyYRDALSLQCLASFLFLYCACMSPVITFGGLLGEATEGRVSAIESLFGASMTGIAYSLFAGQALTILGSTG
ParentalPVLVFEKILFKFCKEYGLSYLSLRASIGLWTATLCIILVATDASSLVCYITRFTEEAFASLICIIFIYEA
PVLVFEKILFKFCK.Y.L.YLSL.A.IGLWTA.LCI.LVATDASSLVCYITRFTEEAF.S.ICIIFIYEA
RetrocopyPVLVFEKILFKFCKDYALPYLSLQACIGLWTAFLCIVLVATDASSLVCYITRFTEEAFTSPICIIFIYEA
ParentalLEKLFELSEAYPINMHNDLELLTQYSCNCVEPHNPSNDTLKEWRESNISASDIIWENLTVSECKSLHGEY
.EKL..L.E.YPI.MH..L.....Y.C.C..P.NP.N.TL..W...NI......W.NLTVSEC...HGE.
RetrocopyIEKLIHLAETYPIHMHSQLDHPSLYYCRCTLPENPNNHTLQYWKDHNIVTAEVHWANLTVSECQEMHGEF
ParentalVGRACGHDHPYVPDVLFWSVILFFSTVTLSATLKQFKTSRYFPTKVRSIVSDFAVFLTILCMVLIDYAIG
.G.ACGH..PY.PDVLFWS.ILFF.T..LS.TLK.FK.S.YFPT.VRS.VSDFAVFLTI..MV.ID..IG
RetrocopyMGSACGHHGPYTPDVLFWSCILFFTTFILSSTLKTFKMSHYFPTRVRSMVSDFAVFLTIFTMVIIDFLIG
ParentalIPSPKLQVPSVFKPTRDDRGWFVTPLGPNPWWTVLAAIIPALLCTILIFMDQQITAVIINRKEHKLKKGC
.P.PKLQVPSVF.PTRDDRGW...P.GPNPWWTV.AAIIPALLCT.LIFMDQQITAVIINRKEHKLKKGC
RetrocopyVPPPKLQVPSVFEPTRDDRGWIINPIGPNPWWTVIAAIIPALLCTSLIFMDQQITAVIINRKEHKLKKGC
ParentalGYHLDLLMVAVMLGVCSIM-GLPWFVA
GYHLDLL.VA.MLGVCSIM.GLPWFVA
RetrocopyGYHLDLLVVAIMLGVCSIM<GLPWFVA

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 0 .07 RPM
SRP051959_heart 0 .00 RPM 20 .98 RPM
SRP051959_kidney 0 .00 RPM 0 .00 RPM
SRP051959_liver 0 .00 RPM 0 .00 RPM
SRP051959_lung 0 .00 RPM 0 .02 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 .04 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_2416 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2416 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2416 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 ENSCJAG00000005614 1 retrocopy
retro_cjac_2416 ,


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