RetrogeneDB ID:

retro_cjac_422

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:77035196..77037288(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000035362
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:HEATR2
Ensembl ID:ENSCJAG00000001527
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_422
GTGCTCGCGCCCCACCTGGACGACACCCTTCGCATGCTGCGCTGCTCCCTGCTCGACTCCTTGGCCGCTGTGCACCGCGA
GAGCTGCAGCTGTGCTGCCGTCCTGGCGCAGGCCACGCCCGACCACTTCCACATGCAATCGGAGTCTCTGATCGGTCCCT
GGTGCAGACCATCTCCCACCAGCACTGGAAGGTCCGTGTGGCCGTCATCGAAGCCACGGGCACGATGATCCAGTTTGGCA
ATGGGAAGTCTGTGGACGACGTGCTTTCCCATTTTGCTCAACGGCTGTTTGACGACGTCCCGCAGGTCCGGCGGGCGGTG
GCTTCTGTGGTGGGCGGCTGGCTGCTGCATCTGCGTGACCGCTACTCCTTCTTCCACAAGCTCATACCTTTGCTGCTCAG
CACCCTTGATGACGAGATGCCCGAGGTCAGGCAGCTGGCTGCTAGCCTCTGGGAGGATGTTGGCCTGCAGTGGCAGAGGG
AGAATGAGGAGGAAGGACCTGAAGGACAAGCTGGACTTTGCCCCTCCCTCCCCCACCCCATTACCCTCCGCATGAGCATC
GCCCCGTGCTGGGCTGTCGGAAGCTCTTCTTCAGGAACCTCTCCAAGATCCTCCCCGCATTGTGCCACGACATCACCGAC
TGGGTGGTGGGGACGCGAGTGAAGTCGGTGCAACTGCTGCCCGTGCTGCTGCTGCATGCCGAGGACCACACCACACAACA
CCTGGAGATCGTCCTCCGGACCCTGTTCCTGGCCTGCGCTGACGAGGAGACAGCCGTGGTCCATAGCTGTTCAAGATCCG
CACAGCTCATAGGGACGTTTGTTAACCCTGAGGTATTTCTGAAGCTGATCTTACCAATGCTGAAGAAGGGGCCCTCCGCC
TCCCTCCTCCTGGTGCTGGACTCCACCATTCAGGGCTGCCCCCGAGAAGCCCTCCAGTCGCACCTAACAGCCATTGCCAC
CGAGCTGGCACAGGCCCACATCTGCCAGGCATCTGTAAACGACCTCTACCTGGAGCGTCTGCTGCTCTGCGTGCAGGCCC
TGGTATCCGTGTGTTGCAAGGACTGCGGCATGGCCAGCTTGCAGCTCATGGACGTGCAGCTGACCATAAAGGCCCTCGCA
GGTTCCACCAGCCTCAGGGACAAGGCGCAGGAGACGATGGACTCGCTGGCCGCTGCGGAGGGCGTCAGCAGCTGCCAGAA
CCTCTATCGCAAGTACCTGGGCCCTCTCCTGGAGCGGGCGACCGCGTCGCACCTCGACTGGTCCGCGCCCTCGCCGGAGC
TCCTGTAGTTCAGTGTCATCATCGCGCAGTCGGGCCCCGCCCTAGGAGAAGCCCTGCCGCACGTCATGCACACGCTCAGG
GCCTGTCTGCAGCCCTCCCGAGACCCGCAGATGCGCCTGAAGCTGTTCTCCATCCTGTCCACTATGCTGCCCAGAGCCGC
GGACACCATCGACTCCCATGGGCAGTTACCTAGCTACCTTGAGATGGTGACAAAGGACATCCTGGCCCCCAATCTGCAGT
GGCATGCAGGGAGGACAGCTGCGGCCATCCGCACGGCCGCCGTGTCCTGCCTCTGGGTGCTCACCAGCGGCGAGGTCCTG
TCGGCCAAGCAGATCCAGGACGTGCAGGAAACACTGATGCCTCAAGTCCTGACCACGCTAGAGGAAGATTCGCAGATGAC
TCGGCTGATCTCCTGCCGTATCATCAACACGTTCTTAAAAACCTTGGGCAGCATGATTGATCCAGATAAACTCAAGATTT
ATCCCGAACTCTTAAAGCATCTAGACGACGTTTCCAATGACGTGAGGATGGCAGCTGCCTCCACCCTGGTGACCTGGCTG
CAGTGTGTGAAGAATGTCGATGGAAAGGCCTACTGTCAGAGCAGCGTCCAGTGCCTGTACAGAGAGCTGCTCGTTCACCT
TGACGATCCAGAGAGCGCCATCCAGGACGCCATTTTAGAGGTCCTCAAGGAGGGCAGCGCCCTGTTCCCAGATCTCCTGG
TGAGGGAGACAGAGGCCGTCATCCACAAACACTGCTCGGCCACCTACTGCGAGCAGCTACTGCAGCATGTGCAGACCATG
CCAGCCACGCAG

ORF - retro_cjac_422 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.46 %
Parental protein coverage: 88.75 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalIKAPHLDDALRVLRCSLLDPFAAVRRESCSCAAALAQATPDHFHMQSESLIGP-LMQTISHQHWKVRVAA
..APHLDD.LR.LRCSLLD..AAV.RESCSCAA.LAQATPDHFHMQSESLIGP.L.QTISHQHWKVRVA.
RetrocopyVLAPHLDDTLRMLRCSLLDSLAAVHRESCSCAAVLAQATPDHFHMQSESLIGP<LVQTISHQHWKVRVAV
ParentalIEATGTVIQFGNGKSVDDVLSHFAQRLFDDVPQVRRAVASVVGGWLLHLRDRYSFFHKLIPLLLSTIDDE
IEATGT.IQFGNGKSVDDVLSHFAQRLFDDVPQVRRAVASVVGGWLLHLRDRYSFFHKLIPLLLST.DDE
RetrocopyIEATGTMIQFGNGKSVDDVLSHFAQRLFDDVPQVRRAVASVVGGWLLHLRDRYSFFHKLIPLLLSTLDDE
ParentalMPEVRQLSASLWEDVGLQWQREN-EE-DLKDKLDFTPP-PPPHYPPHGRCSRHPTLGWDSCIPEFLVSVI
MPEVRQL.ASLWEDVGLQWQREN.EE.DLKDKLDF.PP.PPPHYPPH......P.LG........L....
RetrocopyMPEVRQLAASLWEDVGLQWQRENEEE>DLKDKLDFAPP>PPPHYPPH---EHRPVLGCRKLFFRNLSKIL
ParentalDIWCHGVTCMKLWERSCWYLLLPVCVAHWRHPCLQTLSIILSTETQASEPYKSETVKCCSRSAELIGTFV
...CH..T......R.....LLPV...H......Q.L.I.L.T...A........V..CSRSA.LIGTFV
RetrocopyPALCHDITDWVVGTRVKSVQLLPVLLLHAEDHTTQHLEIVLRTLFLACADEETAVVHSCSRSAQLIGTFV
ParentalNPEVFLKLILPMLKKGPSASGLLVLASTIRGCPREALQPHLKAIATELAQAHICQASENYLFLFILSPEC
NPEVFLKLILPMLKKGPSAS.LLVL.STI.GCPREALQ.HL.AIATELAQAHICQAS.N.L.L..L...C
RetrocopyNPEVFLKLILPMLKKGPSASLLLVLDSTIQGCPREALQSHLTAIATELAQAHICQASVNDLYLERLLL-C
ParentalPQKSVSQCRPQRNWAMGKIRDVIRGIIEISESAQRRDKKAQETMDLLATAEGVSSCQDLYRKYMGPLLER
.Q..VS.C......A.....DV...I.....S...RDK.AQETMD.LA.AEGVSSCQ.LYRKY.GPLLER
RetrocopyVQALVSVCCKDCGMASLQLMDVQLTIKALAGSTSLRDK-AQETMDSLAAAEGVSSCQNLYRKYLGPLLER
ParentalATASHLDWTAHSPELLQFSVIIAQSGPALGEALPHIMPTLRACLQPSRDPQMRLKLFSILSTMLLRAADT
ATASHLDW.A.SPELL.FSVIIAQSGPALGEALPH.M.TLRACLQPSRDPQMRLKLFSILSTML.RAADT
RetrocopyATASHLDWSAPSPELL*FSVIIAQSGPALGEALPHVMHTLRACLQPSRDPQMRLKLFSILSTMLPRAADT
ParentalIDSQGQLPSYLEMVTKDILAPNLQWHAGRTAAAIRTAAVSCLWAFTSSEVLSAKQIRDVQETLMPQVLTT
IDS.GQLPSYLEMVTKDILAPNLQWHAGRTAAAIRTAAVSCLW..TS.EVLSAKQI.DVQETLMPQVLTT
RetrocopyIDSHGQLPSYLEMVTKDILAPNLQWHAGRTAAAIRTAAVSCLWVLTSGEVLSAKQIQDVQETLMPQVLTT
ParentalLEEDSQMTRLISCRIINTFLKTLGSMIDPDKLIKIYPELLKRLDDVSNDVRMAAASTLVTWLQCVKNADG
LEEDSQMTRLISCRIINTFLKTLGSMIDPDKL.KIYPELLK.LDDVSNDVRMAAASTLVTWLQCVKN.DG
RetrocopyLEEDSQMTRLISCRIINTFLKTLGSMIDPDKL-KIYPELLKHLDDVSNDVRMAAASTLVTWLQCVKNVDG
ParentalKAYYQSSIQYLYRELLVHLDDPESAIQDAVLEVLKEGSALFPDLLVRETEAVIHKHRSATYCEQLLQHVQ
KAY.QSS.Q.LYRELLVHLDDPESAIQDA.LEVLKEGSALFPDLLVRETEAVIHKH.SATYCEQLLQHVQ
RetrocopyKAYCQSSVQCLYRELLVHLDDPESAIQDAILEVLKEGSALFPDLLVRETEAVIHKHCSATYCEQLLQHVQ
ParentalAVPATQ
..PATQ
RetrocopyTMPATQ

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 .44 RPM 3 .95 RPM
SRP051959_heart 0 .44 RPM 2 .68 RPM
SRP051959_kidney 0 .64 RPM 5 .88 RPM
SRP051959_liver 0 .17 RPM 1 .26 RPM
SRP051959_lung 0 .59 RPM 4 .31 RPM
SRP051959_lymph_node 0 .34 RPM 2 .76 RPM
SRP051959_skeletal_muscle 0 .28 RPM 2 .25 RPM
SRP051959_spleen 0 .19 RPM 2 .42 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_422 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_422 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_422 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 ENSCJAG00000001527 1 retrocopy
retro_cjac_422 ,


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