RetrogeneDB ID:

retro_cjac_2359

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:4:102943508..102945951(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000001595
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:INO80
Ensembl ID:ENSCJAG00000020770
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2359
TTGATGAGAATCAACATGATTTTGAAGCCATTTATGCTGAGGAGAATCAAGAAAGATGTGGAAAATGAATTATCTGACAA
GATTGAAATTCTAATGTATTGCCAACTGACCAGCCGACATAAGCTTTTATATCAGGTACTAAAGAACAAAATTTCCATTG
AGGATTTATTGCAGTCTTCTATGGGCTCTACTCAACAAGCACAGAATACCACCAGCAGCCTCATGAATCTGGTCATGCAG
TTTAGGAAGGTGTGTAATCACCCAGAGTTATTTGAACAGCAAGAGACTTGGTCTCCATTTCATAATTCCTTAAAGCCATA
CCACATTTCAAAGTTTATCTACTGTCGTGGACAGATCAGGGTCTTCAACCATTCACGAGACAGGTGGTTAAGGGTTCTTT
CTCCATTTGCACCAGACTATATCCAACAGTCTCTCTTTCACAGAAAAGGTCTTAATGAAGAAAGCTGTTTCTCTTTCCTT
TGCTTTATTGATATATCTCCAGCAGAAATGGCAAACTTCATGCTTCAGGGACTTTTGGCCAGATGGTTAGCTCTTTTCCT
GTCTCTGAAAGCCTCCTACAGGCTCCATCAGCTACGCTCCTGGGGAGAGCCAGAAGGGGAGAACCAGCAGAGATACCTGA
GAAACAAGGATTTCCTTCTTGGGGTTAATTTTCCACTCTCCTTTCCAAACCTTTGCAGCTGCCCTTTGTTAAAGTCTCTT
GTTTTCAGCAGCCACTGTAAAGCAGTGAGTGGCTACTCAGACCAGATCATCCATCAGCAGAGATCAGCTACCTCCTCGCT
GCATCGCTGCCTGCTCACTGAGCTGCCGTCTTTTTTGTGTGTGGCCAGCCCACGAGTTACCGCAGTGCCATTGGATTCTT
ACTACAATGACCGAAGTGCAGAATATGAACGGCGAGTTCTGAAGGAAGGAGGGAGTCTGGCAGCCAAGGAGTGTTTGTTG
AATGGGGCTCCTGAACTGGCTGCAGACTGGCTGAATCGGCAATCACAGTTCTTCCCAGAGCCAGCCGGAGGTCTGTGGAG
CATCAGCCTCAGAATGGCTGGTCTTTCATCAGGATTCCAGGCAAGGAGAGCCTCATCACTGACAGTGGAAAGCTGTATGC
CCTTGATGTCCTGCTGACTCGGCTCAAGTCTCAAGGGCATAGGGTCCTTATCTACTCCCAGATGACCAGGATGATAGACC
TGCTGGAGGAATACATGGTGTATAGGAAGCATACCTACATGAGGCTTGATGGCTCATCCAAGATCTCGGAGAGGCGAGAC
ATGGTTGCTGATTTTCAGAACAGGAATGACATCTTTGTGTTCCTGTTAAGCACACGAGCTGGAGGACTGGGTATCAATCT
CACTGCTGCAGACACAGTGATTTTCTATGATAGTGACTGGAACCCCACTGTGGATCAGCAGGCCATGGACAGGGCCCATC
GCTTGGGGCAGACAAAGCAGGTTACCATATACCGACTCATCTGTAAAGGCACCATTGAAGAACGCATTCTGCAAAGAGCC
AAGGAGAAGAGTGAGATTCAGCGGATGGTGATTTCAGGTGGGAACTTCAAAGCAGATACCTTGAAACTCAAAGAAGTGGT
TAGTCTTCTTCTAGACAACGAAGAGTTGGAAAAAAATTGAGGCTACGGCAGGAAGAGAAACGGCAACAGGAGGAAACCAA
CCGAGTGAAAGAGCACAAGTGGAAGCGGGAAAAGTATGCGGAGAAGAAGAAAAAGGAAGATGAATTGGATGGGAAAAGGA
GAAAAGAGGGTGTGAACCTTGTGATCCCATTTGTTCCCTCGGCTGATAACTCCAACCTCTCTGCTGACGGAGATGATTCT
TTTATTAGTGTGGACTCAGCCATGCCAAGCCCTTTCAGTGAGATCTCCATCAGCAGTGAGCTACACACTGGCTCCATTCC
CCTGGATGAGAGTAGCAGTGATATGCTGGTCATTGTGGATGACCCAGCCTCCTCAGCCCCTCAATCTAGAGCTACCAACT
CTCCTGCATCCATAAAAGGCTCCGTCTCAGACACCGTGAATGGAATCTCCATTCAGGAAATGCCAGCTGCAGGACGTGGT
CACTCAACCCGAAGCCGAGGCCGCCCCAAAGGTTCAGGAAGCACAGCCAAAGGAGCAGGGAAGGGCAGGAGCCGAAAGTC
CACAGCAGGCAGCGCTGCTGCAATGGCAGGAGCCAAAGCTGGGGCTGCAGCATACGCGTACAACGTGTCTAAAGGAATCT
CCGCCAGCAGTCTGCAGACGTCCCTTGTCCGGCCTGCTGGCCTTGCTGACTTTGGACCTTCAAGCGCCTCTTCTCCTTTG
AGTTCCCCTTTGAGCAAAAGAAACAATGTTCCTGGGACTCCCAAAAACCTCCACATGACCAGCAGCCTAGCCCCAGACTC
TCTGGTCCAGAAACAGGGCAAAGGCAACCCCTCTGGAGGACGG

ORF - retro_cjac_2359 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 93.7 %
Parental protein coverage: 52.96 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalLSRLHMILKPFMLRRIKKDVENELSDKIEILMYCQLTSRQKLLYQALKNKISIEDLLQSSMGSTQQAQNT
L.R..MILKPFMLRRIKKDVENELSDKIEILMYCQLTSR.KLLYQ.LKNKISIEDLLQSSMGSTQQAQNT
RetrocopyLMRINMILKPFMLRRIKKDVENELSDKIEILMYCQLTSRHKLLYQVLKNKISIEDLLQSSMGSTQQAQNT
ParentalTSSLMNLVMQFRKVCNHPELFERQETWSPFHISLKPYHISKFIYRRGQIRVFNHSRDRWLRVLSPFAPDY
TSSLMNLVMQFRKVCNHPELFE.QETWSPFH.SLKPYHISKFIY.RGQIRVFNHSRDRWLRVLSPFAPDY
RetrocopyTSSLMNLVMQFRKVCNHPELFEQQETWSPFHNSLKPYHISKFIYCRGQIRVFNHSRDRWLRVLSPFAPDY
ParentalIQQSLFHRKGINEESCFSFLRFIDISPAEMANFMLQGLLARWLALFLSLKASYRLHQLRSWGEPEGENQQ
IQQSLFHRKG.NEESCFSFL.FIDISPAEMANFMLQGLLARWLALFLSLKASYRLHQLRSWGEPEGENQQ
RetrocopyIQQSLFHRKGLNEESCFSFLCFIDISPAEMANFMLQGLLARWLALFLSLKASYRLHQLRSWGEPEGENQQ
ParentalRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQIIHQQRSATSSLRRCLLTELPSFLC
RYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQIIHQQRSATSSL.RCLLTELPSFLC
RetrocopyRYLRNKDFLLGVNFPLSFPNLCSCPLLKSLVFSSHCKAVSGYSDQIIHQQRSATSSLHRCLLTELPSFLC
ParentalVASPRVTAVPLDSYCNDRSAEYERRVLKEGGSLAAKECLLNGAPELAADWLNRRSQFFPEPAGGLWSI-R
VASPRVTAVPLDSY.NDRSAEYERRVLKEGGSLAAKECLLNGAPELAADWLNR.SQFFPEPAGGLWSI..
RetrocopyVASPRVTAVPLDSYYNDRSAEYERRVLKEGGSLAAKECLLNGAPELAADWLNRQSQFFPEPAGGLWSI<Q
ParentalPQNGWSFIRIPGKESLITDSGKLYALDVLLTRLKSQGHRVLIYSQMTRMIDLLEEYMVYRKHTYMRLDGS
PQNGWSFIRIPGKESLITDSGKLYALDVLLTRLKSQGHRVLIYSQMTRMIDLLEEYMVYRKHTYMRLDGS
RetrocopyPQNGWSFIRIPGKESLITDSGKLYALDVLLTRLKSQGHRVLIYSQMTRMIDLLEEYMVYRKHTYMRLDGS
ParentalSKISERRDMVADFQNRNDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTVDQQAMDRAHRLGQTKQVT
SKISERRDMVADFQNRNDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTVDQQAMDRAHRLGQTKQVT
RetrocopySKISERRDMVADFQNRNDIFVFLLSTRAGGLGINLTAADTVIFYDSDWNPTVDQQAMDRAHRLGQTKQVT
ParentalVYRLICKGTIEERILQRAKEKSEIQRMVISGGNFKPDTLKPKEVVSLLLDDEELEK-KLRLRQEEKRQQE
.YRLICKGTIEERILQRAKEKSEIQRMVISGGNFK.DTLK.KEVVSLLLD.EELEK.KLRLRQEEKRQQE
RetrocopyIYRLICKGTIEERILQRAKEKSEIQRMVISGGNFKADTLKLKEVVSLLLDNEELEK<KLRLRQEEKRQQE
ParentalETNRVKERKRKREKYAEKKKKEDELDGKRRKEGVNLVIPFVPSADNSNLSADGDDSFISVDSAMPSPFSE
ETNRVKE.K.KREKYAEKKKKEDELDGKRRKEGVNLVIPFVPSADNSNLSADGDDSFISVDSAMPSPFSE
RetrocopyETNRVKEHKWKREKYAEKKKKEDELDGKRRKEGVNLVIPFVPSADNSNLSADGDDSFISVDSAMPSPFSE
ParentalISISSELHTGSIPLDESSSDMLVIVDDPASSAPQSRATNSPASITGSVSDTVNGISIQEMPAAGRGHSAR
ISISSELHTGSIPLDESSSDMLVIVDDPASSAPQSRATNSPASI.GSVSDTVNGISIQEMPAAGRGHS.R
RetrocopyISISSELHTGSIPLDESSSDMLVIVDDPASSAPQSRATNSPASIKGSVSDTVNGISIQEMPAAGRGHSTR
ParentalSRGRPKGSGSTAKGAGKGRSRKSTAGSAAAMAGAKAGAAAASAAAYAAYGYNVSKGISASSPLQTSLVRP
SRGRPKGSGSTA....KG........S.A..A.A.AGA.A......AAY.YNVSKGISASS.LQTSLVRP
RetrocopySRGRPKGSGSTA----KGAGKGRSRKSTAGSAAAMAGAKAGA----AAYAYNVSKGISASS-LQTSLVRP
ParentalAGLADFGPSSASSPLSSPLSKGNNVPGTPKNLHMTSSLAPDSLVRKQGKGNPSGGR
AGLADFGPSSASSPLSSPLSK.NNVPGTPKNLHMTSSLAPDSLV.KQGKGNPSGGR
RetrocopyAGLADFGPSSASSPLSSPLSKRNNVPGTPKNLHMTSSLAPDSLVQKQGKGNPSGGR

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 28 .00 RPM
SRP051959_heart 0 .00 RPM 24 .45 RPM
SRP051959_kidney 0 .02 RPM 30 .79 RPM
SRP051959_liver 0 .00 RPM 20 .14 RPM
SRP051959_lung 0 .10 RPM 37 .89 RPM
SRP051959_lymph_node 0 .05 RPM 40 .71 RPM
SRP051959_skeletal_muscle 0 .02 RPM 20 .00 RPM
SRP051959_spleen 0 .06 RPM 35 .32 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_2359 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2359 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2359 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 ENSCJAG00000020770 1 retrocopy
retro_cjac_2359 ,


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