RetrogeneDB ID:

retro_cjac_3958

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL286426.1:206142..208528(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:SLIT1
Ensembl ID:ENSCJAG00000036372
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3958
TTTAGGCCTCTGCGGGCCATCTAGACACTTTTTCTAGCCCAGAACCTTTCATTTGCTATTGTAATCTCAAGTGGCTGGCC
GACTTTCTGCACACCAATCCCATCAAGATGAGTGGGGCCCGCTGTGCCAGTCCCTGGCTCCTTGCCAACAAGCGCATTGA
GCAGATCAAGAGCAAGAAGTTCCGATGCTCAGCCAAAGAGCAGTACTTCATTTCAGGCATGGAGGATTACCAGCTGAACA
GCGAGCGCAACATCTAGGTGGTGTGTCCATATAAGTGCTGCTGTGAGGCCAGCATGGTGGCGTGCTACAGCCTGAAGCTC
ACCAAGATTTTCGAGCGCATTCCCCAGTCCACGGCTGAACTGCAATTGAATAACCATGAGATTTTCATCCTGGAGGCCAC
CGGGATGCTTAAAACACACATCTGAAGAAAATCAACCTGAGCAACTGCAAGATGTCAGAAATTGAAGACAGGGCCTTCGA
GGGTGCAGCCTCTGTGAGCGAGCTGCACCTGACTGCCAACCAGCTGGAGTCCATCCAGAGCAGCATGTTCTGGGGTCTGG
ATGGCCTGAGGACCCAAATGCTGCAGGACAAAGGCATCAGCTGCATCCACAATGACAGCTTCACGGGCCTGCACAATGTC
CGGCTGCTCTCGCTCTATAAAAACCAGATCACCACCGTGTCCCCAGGGGCCTTTGACACCCTCCAGTTTCTCTCCAGGCT
GATCCTCCTGGCCAACTTTTTCAACTGCAACTGCCAGCTGGCTTGGCTGGGAGATTGGCTGCGGAAGCGCAAGATTGTGA
CGGGGAACCCTCGCTGCCAGAACCACGACTTCTTGTGGCAGATTCCCCTGCAAAATGTGGCCTTCCCTGACTTCAGGTGT
TAGAAAGGCCAGAAGGAGGGGGGCTGCCTGCCCCACCCTCAGTGCCCACAGGAGTGCACCTGCTTGGACACCATGGTCTG
GTGCAGCACCAAGCACCTGTGGGCCCTGCCCAGGGATGTCCCCAAAGATGTCACAGAACTCTATTTGGATGGGAACCAGT
TCACGCTTGTTCCAGGACAGCTGTTTACCTTCAAGTACCTGCAGCTCGTGGACTTGAGCAACAACGAGATCAGTTTTTTA
AGCAATTTTTCCCTCACCAACATAAGCCAGCTGACCACTCTGATCCTCAGCTACAATGCCCTGCAGTGCATCCCGCCACT
GGCCTTCCAAAGACTCCACTCTTTGCAGCTACTGTCCCTCCATGGCAATGACATCTCCACCTTCAGAGAGGGCATCTTTG
CAGACATGACCTTCCTGTCTTACCTGGCCAATTGGTGCCAACCCCCTTTACTGTGACTGCCACCTCCACTGGCTGTCCAG
CTGGGTGAAGACTGGCTACTAGGAACCGGGCATTGCCTGCTGTGCTGGGCCCCCAGACGTGGAGCGCAAGCTGCTCCTCA
CCATGCCTGCCAAGAAGTTTGAATGCCAAGGTTTTCCCACACTGGCCGTCCAGGCCAAGTGTGATCCCTGCTTGTCCAGT
CCCTGCCAGAACCAGGGCACCTGCCACAATGACCCTCTTGAGGTGTACAGGTGTGCTTTCCCCAGCAGCTATAAGGGCTG
AGACTGTGAGGTATTTCTGGACAGCTGTTCCAGTGGCCCCTGTGAAAACAAGGACACCTGCCATGCACAGGAGGGTGAGG
ATGCCCAATTCACGTGCTCCTGTCCCACTAGCTTTGAAAAACCAACCTGTGGGGTGAACATGAATGACTGAGTGAAGCAT
GCCTGTGCCAATGGGGGCATCTGCCTGGACAGCGTGGGCAACTACACCTGCCAGTGCCCTCTGCAGTACAAGGGAAGGGC
CTGTGAGCAGCCGGTGGACTTGTGCCCTCCGAATCTGAACCCATGTCAACATGAGGCCCAGTGTGTGGGCACCCCAGCTG
GGCCCAGGTGTGAGTGTGTGCCAGGTTATGAAGGTGATAACTGCAGTAAGAACCAGGATGACTGCAGGAACCACCACTGC
CAGAATGGAGCACAGTGTGTGGATGAAGTCAACAGCTACTTCTGCCTCTGTGCTGAGGGCTACAGCTGACAGCTCTGTGA
GATCCCTCCCCATCCACCTGCCCCCAAGAGCCCCTGTGAGGGGATTGGGTGCCAGAATGAGGCCAACTGTGTGGACCAGG
GCAACAGGTCCATGTTCCAGTGCCTCCCAGGCTTCGATGGCCCTGAGTGTGAGAAGTTGCTCAGTGCAACTTTGTGGATC
TGGATGCTTACCTGCAGTTTACTGACCTGCAAAACTGGCCACGGGCCAACATCACCCTGCAGGTTTTCATGGTAGAGAAC
AATGGAATCCTTTTGTATAATGGGGACAACGATCACATTGCAGTTGAACTGTACCAGGGCCATGTG

ORF - retro_cjac_3958 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.97 %
Parental protein coverage: 56.44 %
Number of stop codons detected: 9
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalFTSLRAIQTLHLAQN-PFICDCNLKWLADFLRTNPIETSGARCASPRRLANKRIGQIKSKKFRCSAKEQY
F..LRAI.TL.LAQN.PFIC.CNLKWLADFL.TNPI..SGARCASP..LANKRI.QIKSKKFRCSAKEQY
RetrocopyFRPLRAI*TLFLAQN<PFICYCNLKWLADFLHTNPIKMSGARCASPWLLANKRIEQIKSKKFRCSAKEQY
ParentalFIPGTEDYQLNHEFVYTYVYAHR-CLQASVIYICKFFMAFLMDLKCPSFVDVRLNNNEISILEATGMFKK
FI.G.EDYQLN.E.....V.....C..AS..................S.....LNN.EI.ILEATGM.K.
RetrocopyFISGMEDYQLNSERNI*VVCPYKCCCEASMVACYSLKLTKIFERIPQSTAELQLNNHEIFILEATGMLK-
ParentalLTHL-KKINLSNNKVSEIEDG-AFEGAASVSELHLTANQLESIRSGMFRGLDGLRTLMLRNNRISCIHND
.TH...K.............G.AFEGAASVSELHLTANQLESI.S.MF.GLDGLRT.ML....ISCIHND
Retrocopy-THI*RKST*ATARCQKLKTG<AFEGAASVSELHLTANQLESIQSSMFWGLDGLRTQMLQDKGISCIHND
ParentalSFTGLRNVRLLSLYDNQITTVSPGAFDTLQSLSTLNLLANPFNCNCQLAWLGDWLRKRKIVTGNPRCQNP
SFTGL.NVRLLSLY.NQITTVSPGAFDTLQ.LS.L.LLAN.FNCNCQLAWLGDWLRKRKIVTGNPRCQN.
RetrocopySFTGLHNVRLLSLYKNQITTVSPGAFDTLQFLSRLILLANFFNCNCQLAWLGDWLRKRKIVTGNPRCQNH
ParentalDFLRQIPLQDVAFPDFRCEEGQEEGGCLPRPQCPQECACLDTVVRCSNKHLRALPRGVPKNVTELYLDGN
DFL.QIPLQ.VAFPDFRC..GQ.EGGCLP.PQCPQEC.CLDT.V.CS.KHL.ALPR.VPK.VTELYLDGN
RetrocopyDFLWQIPLQNVAFPDFRC*KGQKEGGCLPHPQCPQECTCLDTMVWCSTKHLWALPRDVPKDVTELYLDGN
ParentalQFTLVPGQLFTFKYLQLVDLSNNKISSLSNSSFTNMSQLTTLILSYNALQCIPPLAFQGLRSLRLLSLHG
QFTLVPGQLFTFKYLQLVDLSNN.IS.LSN.S.TN.SQLTTLILSYNALQCIPPLAFQ.L.SL.LLSLHG
RetrocopyQFTLVPGQLFTFKYLQLVDLSNNEISFLSNFSLTNISQLTTLILSYNALQCIPPLAFQRLHSLQLLSLHG
ParentalNDISTLREGIFADVTSLSHLA-IGANPLYCDCHLRWLSSWVKTGYKEPGIARCAGPPDMEGKLLLTTPAK
NDIST.REGIFAD.T.LS.LA.IGANPLYCDCHL.WLSSWVKTGY.EPGIA.CAGPPD.E.KLLLT.PAK
RetrocopyNDISTFREGIFADMTFLSYLA>IGANPLYCDCHLHWLSSWVKTGY*EPGIACCAGPPDVERKLLLTMPAK
ParentalKFECQGKPRIGVGEKGFLCFSVAAGSSGYLHSQCILEMLEGSAIAGRQGRDCEVSLDSCSSGPCENGGTC
KFECQG.P...V..K...C.S......G..H....LE...........G.DCEV.LDSCSSGPCEN..TC
RetrocopyKFECQGFPTLAVQAKCDPCLSSPCQNQGTCHND-PLEVYRCAFPSSYKG*DCEVFLDSCSSGPCENKDTC
ParentalHAQEDEDAPFTCSCPTGFEGPTCGVNTDDCVEHACANGGICVDGVGNYTCQCPLQYEGRACEQLVDLCSP
HAQE.EDA.FTCSCPT.FE.PTCGVN..D.V.HACANGGIC.D.VGNYTCQCPLQY.GRACEQ.VDLC.P
RetrocopyHAQEGEDAQFTCSCPTSFEKPTCGVNMND*VKHACANGGICLDSVGNYTCQCPLQYKGRACEQPVDLCPP
ParentalDLNPCQHKAQCVGTPDGPRCECVPGYAGDNCSENQDDCRDHRCQNGAQCVDEVNSYSCLCAEGYSGQLCE
.LNPCQH.AQCVGTP.GPRCECVPGY.GDNCS.NQDDCR.H.CQNGAQCVDEVNSY.CLCAEGYS.QLCE
RetrocopyNLNPCQHEAQCVGTPAGPRCECVPGYEGDNCSKNQDDCRNHHCQNGAQCVDEVNSYFCLCAEGYS*QLCE
ParentalIPPHPPAPKSPCEGTECQNGANCVDQGNRPVCQCLPGFGGPECEKLLSV-NFVDRDTYLQFTDLQNWPRA
IPPHPPAPKSPCEG..CQN.ANCVDQGNR...QCLPGF.GPECEKLLS..NFVD.D.YLQFTDLQNWPRA
RetrocopyIPPHPPAPKSPCEGIGCQNEANCVDQGNRSMFQCLPGFDGPECEKLLSA<NFVDLDAYLQFTDLQNWPRA
ParentalNITLQVSTAEDNGILLYNGDNDHIAVELYQGHV
NITLQV...E.NGILLYNGDNDHIAVELYQGHV
RetrocopyNITLQVFMVENNGILLYNGDNDHIAVELYQGHV

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 .27 RPM
SRP051959_heart 0 .00 RPM 0 .81 RPM
SRP051959_kidney 0 .00 RPM 0 .11 RPM
SRP051959_liver 0 .00 RPM 0 .15 RPM
SRP051959_lung 0 .00 RPM 0 .26 RPM
SRP051959_lymph_node 0 .00 RPM 0 .32 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .17 RPM
SRP051959_spleen 0 .00 RPM 0 .15 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_3958 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3958 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3958 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 ENSCJAG00000036372 1 retrocopy
retro_cjac_3958 ,


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