RetrogeneDB ID:

retro_cjac_619

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:136486068..136488311(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:NUP133
Ensembl ID:ENSCJAG00000011040
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_619
ATGATCCCAAACTTTTCAAACCAGACTGCATGTCTGTATAACGAAAGTGCTATCTATGTGTGCTCCACAGGAACTGGGAG
ATTTTCTCTTCCCCAGGAGAAAACTGTCTTCAATGCACAAGGAGATAGTGTTTTAGGTGCTGGTGCCTTTGGTGGTGTTC
CTATCATTTTTTCTAGAAACAGTGGACTAGTGTCTATTACTTCAAGGGAAAATGTGTCCATATTGACAGAAGACCTGGAA
GAGTCCTTAGCATCTTCAGTTGCTGGACCAAACAATGTGAGTATGGTTTTTGAGACCACTCCAAAGAATGAAACTATAGC
CCAGGAAGATAAAATCAAGTTGCTGAAAGCTGCCTTTCTGCAATACTGCAGGAAAGATTTAGGTCATGCTCAAATGGTGG
TTGAAGAGCTCTTTTCTTCTCACTCTGATTTGGATTCTGATTCTGAACTAGACAGGGCAGTTACCCAAATCAGTGTAGAC
CTGATGGATGACTACCCAGTGTCTGACCCATGGTGGGCTGAGTCTGTCCCTGAGGAAGTACCTGGGTTCAGCAACGCATC
ACTGATTATTCTTCACCAGCTAGAAGACAAGATGAAAGCTCGCTCTTTCCTTATGGACTTTATTCATCAAGTTGGCTTAT
TTGGATGTCTAGGCAGTTTTCTAGTTAGAGGGACACCGATGACCACTTGACTGTTGCTCTGTGAGCATGTGGAAAAGCTG
TCAGCCACCATTTTTCTCAAGAACCACCACTCCCGGCTTTCTGACCTTGTCAACACAGCCATATTGAACAAGAGGGAGTA
TGAAATTTCATCCAACCTGACTCCTGCAGATGTATTTTTCAGGGAGGTATCCCAAGTAGATACCATCTGCGAGTGCTTAC
TGGAGCATGAGGAGCAAGTCTTGAGGGATACACCTTTGGATTCCGTTGAATGGACTGAAGTGGTGATCAACGTGAACAAT
ATTCTCAAGGATATGCTGCAGGCTGCTAGTCATTATCACCAAAATAGAAACTCTTTGTATAGAAAAGAAGAACCACCAGA
GAAAGAACTTGAATATGTTCCATGGATGGCAATGAGTGGTCCTGGTGGCATCCAAACAGTAATAATGCACCAGCATGAGA
TTGTCCTGAGGGTGGTTTATCCACAGGCAGACAGCAACCTCTGAAACATCGTGACTGAGCAACTGGTAGCACTGATTGAT
TGCCTCCTAGATGGTTATGTTTCTCAGCTTAAGTCTGTGGAAAGATTGTCCTATCTTTCCAGTAATCAGGAAAGATAGGA
CAATCTGGAGATGGAAAACCTACAGAAAAGATCGGATCTTTTATCTCCTCTTGTTACACTAGGCCAGTACCTGTGGGCTG
CTTCTCTAGCAGAGAAATACTGTGACTTTGATATCTTGGTATAAATGTGTGAGCAAACTGACAACCAGAGCCGACTCCAG
CGCTACATGACCCAGTTTGCTGATCAGAATTTTTCAGACTTTCTCTTCCGTTGGTATCTGGAGAAAGGAAAGCGAGGCAA
ATTATTATCTCAGCCCATTTCTCAGCATGGACAGTTGGCCAATTTTTTGCAAGCTCATGAACATCTCAGCTGGTTACATG
AAATTAATAGCCAAGAATTAGAAAAGGCTCATGCAACACTTCTGAGTTTGGCAAATATGGAAACTTGTTACTTTGCGAAG
AAAAAAACCCTTCTTGGCTTGAGTAAATTGGCTGCATTAGCTTCAGACTTTTCAGAGGATATACTGCAAGAAAAAATGGA
AGAAATGGCTGAGCAAGAGCGCTTCTACTGCATCAGGAGACCCTACCTGAACAGCTGCTAGCGGAGAAACAGCTCAGTGT
GATGCCAGTATTGACCACAAAGCAACTCATTGGTCTATATATCTGTGAAGAAAATAGAAGAGCTAATGAATATGATTTCA
AGAAAGCTTTGGACTTGCTGGAATATATTGATGAGGAAGAAGATGTAAATATAAGTGATCTAAAACTGGAGATCCTTTGC
AAAGCTCTTCAGAGAGATAACTGGTCCAGTTCTGATGGCAAAGATGATCCAATTGAAGTATCTAAAGACAGCATATTTGT
GAAGATCTTACAGAAACTTTTAAAAGATGGCATTTGGCTCAGTGAGTACTTACCAGAAGTGAAAGACCTGTTACAAGCAG
ATCAGCTTGGAAGCTTAAAGTCCAATCTTTACTTCGAGTTTGTTTTGAAAGCAAATTATGACTATTATGTTCGGGGGCAA
ATA

ORF - retro_cjac_619 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.24 %
Parental protein coverage: 64.79 %
Number of stop codons detected: 4
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalMIPNFSNQTACLYNESTIYVCSTGTGRFSLPQEKIVFNAQGDSVLGAGAFGGVPIIFSRNSGLVSITSRE
MIPNFSNQTACLYNES.IYVCSTGTGRFSLPQEK.VFNAQGDSVLGAGAFGGVPIIFSRNSGLVSITSRE
RetrocopyMIPNFSNQTACLYNESAIYVCSTGTGRFSLPQEKTVFNAQGDSVLGAGAFGGVPIIFSRNSGLVSITSRE
ParentalNVSILAEDLEDSLASSVAGPNNVSMVFETTPKNETIAQEDKIKLLKAAFLQYCRKDLGHAQMVVEELFSS
NVSIL.EDLE.SLASSVAGPNNVSMVFETTPKNETIAQEDKIKLLKAAFLQYCRKDLGHAQMVVEELFSS
RetrocopyNVSILTEDLEESLASSVAGPNNVSMVFETTPKNETIAQEDKIKLLKAAFLQYCRKDLGHAQMVVEELFSS
ParentalHSDLDSDSELDRAVTQISVDLMDDYPASDPRWAESVPEEVPGFSNASLIILHQLEDKMKAHSFLMDFIHQ
HSDLDSDSELDRAVTQISVDLMDDYP.SDP.WAESVPEEVPGFSNASLIILHQLEDKMKA.SFLMDFIHQ
RetrocopyHSDLDSDSELDRAVTQISVDLMDDYPVSDPWWAESVPEEVPGFSNASLIILHQLEDKMKARSFLMDFIHQ
ParentalVGLFGRLGSFLVRGTPMATRLLLCEHAEKLSAAIVLKNHHSRLSDLVNTAILIALNKREYEIPSNLTPAD
VGLFG.LGSFLVRGTPM.T.LLLCEH.EKLSA.I.LKNHHSRLSDLVNTAIL...NKREYEI.SNLTPAD
RetrocopyVGLFGCLGSFLVRGTPMTT*LLLCEHVEKLSATIFLKNHHSRLSDLVNTAIL---NKREYEISSNLTPAD
ParentalVFFREVSQVDTICECLLEHEEQVLRDTPLDSVEWAEVVINVNNILKDMLQAASHYRQHRNSLYRKEEPPE
VFFREVSQVDTICECLLEHEEQVLRDTPLDSVEW.EVVINVNNILKDMLQAASHY.Q.RNSLYRKEEPPE
RetrocopyVFFREVSQVDTICECLLEHEEQVLRDTPLDSVEWTEVVINVNNILKDMLQAASHYHQNRNSLYRKEEPPE
ParentalKELEYVPWTATSGPGGIRTVIMRQHEIVLRVVYPQADSNLRNMVTEQLVALIDCFLDGYVSQLKSVDK--
KELEYVPW.A.SGPGGI.TVIM.QHEIVLRVVYPQADSNL.N.VTEQLVALIDC.LDGYVSQLKSV....
RetrocopyKELEYVPWMAMSGPGGIQTVIMHQHEIVLRVVYPQADSNL*NIVTEQLVALIDCLLDGYVSQLKSVERLS
Parental--SSNQERYDNLEMEYLQKRSDLLSPLLTLGQYLWAASLAEKYCDFDILVQMCEQTDNQSRLQRYMTQFA
..SSNQER.DNLEME.LQKRSDLLSPL.TLGQYLWAASLAEKYCDFDILV.MCEQTDNQSRLQRYMTQFA
RetrocopyYLSSNQER*DNLEMENLQKRSDLLSPLVTLGQYLWAASLAEKYCDFDILV*MCEQTDNQSRLQRYMTQFA
ParentalDQNFSDFLFHWYLEKGKRGKLLSQPISQHGQLANFLQAHEHLSWLHEINSQELEKAHATLLGLANMETRY
DQNFSDFLF.WYLEKGKRGKLLSQPISQHGQLANFLQAHEHLSWLHEINSQELEKAHATLL.LANMET.Y
RetrocopyDQNFSDFLFRWYLEKGKRGKLLSQPISQHGQLANFLQAHEHLSWLHEINSQELEKAHATLLSLANMETCY
ParentalFAKKKTLLGLSKLAALASDFPEDILQEKIEEMAEQERF-LLHQETLPEQLLAEKQLNLSAMPVLTAKQLI
FAKKKTLLGLSKLAALASDF.EDILQEK.EEMAEQERF.LLHQETLPEQLLAEKQ..LS.MPVLT.KQLI
RetrocopyFAKKKTLLGLSKLAALASDFSEDILQEKMEEMAEQERF<LLHQETLPEQLLAEKQ--LSVMPVLTTKQLI
ParentalGLYICEENRRANEYDFKKALDLLEYIDEEEDVNISDLKLEILCKALQRDNWSSSDGKDDPIEVSKDSIFV
GLYICEENRRANEYDFKKALDLLEYIDEEEDVNISDLKLEILCKALQRDNWSSSDGKDDPIEVSKDSIFV
RetrocopyGLYICEENRRANEYDFKKALDLLEYIDEEEDVNISDLKLEILCKALQRDNWSSSDGKDDPIEVSKDSIFV
ParentalKILQKLLKDGIRLSEYLPEVKDLLQADQLGSLKSNPYFEFVLKANYEYYVQGQI
KILQKLLKDGI.LSEYLPEVKDLLQADQLGSLKSN.YFEFVLKANY.YYV.GQI
RetrocopyKILQKLLKDGIWLSEYLPEVKDLLQADQLGSLKSNLYFEFVLKANYDYYVRGQI

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 1 .60 RPM 20 .06 RPM
SRP051959_heart 2 .51 RPM 27 .91 RPM
SRP051959_kidney 1 .22 RPM 28 .60 RPM
SRP051959_liver 2 .77 RPM 20 .25 RPM
SRP051959_lung 2 .90 RPM 20 .64 RPM
SRP051959_lymph_node 1 .89 RPM 25 .68 RPM
SRP051959_skeletal_muscle 0 .79 RPM 36 .73 RPM
SRP051959_spleen 2 .37 RPM 28 .49 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_619 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_619 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_619 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 ENSCJAG00000011040 1 retrocopy
retro_cjac_619 ,


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