RetrogeneDB ID:

retro_cjac_4088

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:71702970..71704929(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000011516
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TNFRSF21
Ensembl ID:ENSCJAG00000011904
Aliases:None
Description:tumor necrosis factor receptor superfamily, member 21 [Source:HGNC Symbol;Acc:13469]


Retrocopy-Parental alignment summary:






>retro_cjac_4088
ATGGGGACCTCTGCGAGCAGCAGCACCGCTCTCGCCTCCGGCAGCCTCTTCGCCCGCCGAACCAGAGCCACGATGATCGC
GGGATCCCTTCTCCTGCTTGGATTCCTTAGCACCACCACAGCTCAGCCGGAACAGAAGGCCTCAAATCTCATTGGCACAT
ACCGCCATGCTGACCTTGCCACCGGCCAAGTGCTAACCTGTGACAAGTGTCCAGCAGGAACCTATGTCTCTGAGCATTGT
ACCAACACAAGCCTGCGCGTCTGCAGCCGTTGCCCTGTGGGGACCTTTACCAGGCATGAGAATGGCATAGAGAAATGCCA
TGACTGTAGTCAGCCATGCCCATGGCCAATGATTGAGAAATTACCTTGTGCTGCCTTGACTGACCGAGAATGCGCTTGCC
CACCTGGCATGTTCCAGTCTAACGCTACCTGTGCCCCCCATACGGTGTGTCCCGTGGGTTGGGGGGTACGGAAGAAAGGG
ACAGAGACTGAGGATGTGCGGTGTAAGCAGTGTGCTCGGGGTACCTTCTCAGATGTGCCTTCTAGTGTGATGAAATGCAA
AGCATACACAGACTGTCTGAGTCAGAAACTGGTGGTGATCAAGCCGGGGACCAAGGAGGCAGACAACGTCTGTGGCACAC
TCCCACCCTTCTCCAGCTCCACCTCACCTTCCCCTGGCACAGCCATCATTTCACGCTCTGAGCACATGGAATCCCATCAA
GTCCCTTCCTCCACTTATGTTCCCAAAGGCATGAACTCAACAGAATCCAACTCTTCTGCCTCTCTTGGACCAAAGGTATC
GAGTAGCATCCAGGAAGGAACAGTCCCTGACAATACAGGCTCTGCAAGGGGGAAGGAAGACATGAACAAGACGCTCCCAA
ACCTTCAGGTAGTCAACCACCAGCAAGGCCCCCACCACAGACACATTTTGAAGCTGCTGCCATCCACGGAGGCCCCTGGG
GGTGAGAAGTCCAGCACGCCCATGAAGGGCTCCAAGAGGGGACATCCTAGACAGAACCTACAAAACCATTTTGACATCAA
CGAACATTTTCCCTGGATGATTGTGCTTTTCCTGCTGCTGGTGCTTGTGGTGATTGTAGTGTGCAGCATCCAGAAAAGCT
CGAGGACTCTAAAAAAGGGGCCCCGACAGGATCCCAGTGCCACTGTGGAAAAGGTAGGGCTAAAGAAATCCATGACTCGA
ACCCAGAACAGGGAGAAGTGGATATACTACTGCAATGGCTATGGTACCGACATCCTGATGCTTGTAGCAGCCCAAGTGGG
AAGCCAGTGGAAAGATATCTATCAATTTCTTTGCAATGTCAGTGAGAGGGAGGTTGCTGCTTTTTCCAACGGGTGCACAG
CTGACCACGAGCGGGCCTACGCGGCTCTGCAGCACTGGGCCATCCAGTGCCCCGAGGCCAGCCTCGCCCAGCTGATTAGC
GCCCTGCGCCAGCACCGGAGAAACGATGTTGTGGAGAAGATTCGTGGGCTTATGGAAGACACCACCCAGCTGGAAACTGA
CAAACTGGCTCTCCGGATGAGCCGCCGCCTGCTTAGTCCCAGCCCCAGCTCCAATGCAAAACTTGAGAATTCCACTCTCC
GGACAGTGGTGCCTTCCCCGCTGGACAAGAACAAGGGCTTCTTCGTGGGTGAGTCAGAGCCCCTTCTCCGCTGTGTCTTT
ACATCCAGTGGCTCCTCCACGCTGAACAGGAACGGTTCCTTTATTACCAAAGAAAAGAAGGACACAGTGTTGCGGCAGGT
ACGCCTGGACCCCTGTGACTTGCAGCCTATCTTTGATGACATGCTCCACATTCTAAATCCTGAGGAGCTGCGAGTGATTG
AAGAGATTCCCCAGGCTGAGGACAAACTGGACCAGCTATTCGAAATTATTGGAGTCAAGAGCCAGGAAGCCAGCCACACC
CTCCTGGACTCTGTTTATAGCCATCTTCCTGACCTGCTG

ORF - retro_cjac_4088 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 91.76 %
Parental protein coverage: 100. %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGTSASSSTVLASGSRFARRATATMIAGSLLLLGFLSTTTAQPEQKASNLIGTYRHVDRATGQVLTCDKC
MGTSASSST.LASGS.FARR..ATMIAGSLLLLGFLSTTTAQPEQKASNLIGTYRH.D.ATGQVLTCDKC
RetrocopyMGTSASSSTALASGSLFARRTRATMIAGSLLLLGFLSTTTAQPEQKASNLIGTYRHADLATGQVLTCDKC
ParentalPAGTYVSEHCTNTSLRVCSRCPVGTFTRHENGIEKCHDCSQPCPWPMIEKLPCAALTDRECTCPPGMFQS
PAGTYVSEHCTNTSLRVCSRCPVGTFTRHENGIEKCHDCSQPCPWPMIEKLPCAALTDREC.CPPGMFQS
RetrocopyPAGTYVSEHCTNTSLRVCSRCPVGTFTRHENGIEKCHDCSQPCPWPMIEKLPCAALTDRECACPPGMFQS
ParentalNATCAPHTVCPMGWGVRKKGTETEDVRCKQCARGTFSDVPSSVMKCKAYTDCLSQNLVVIKPGTKEADNL
NATCAPHTVCP.GWGVRKKGTETEDVRCKQCARGTFSDVPSSVMKCKAYTDCLSQ.LVVIKPGTKEADN.
RetrocopyNATCAPHTVCPVGWGVRKKGTETEDVRCKQCARGTFSDVPSSVMKCKAYTDCLSQKLVVIKPGTKEADNV
ParentalCGTLPPFSSSTSPSPATAIFSASEHMESHEVPSSTYVPKGMNSTESNSSASVRPKVPSSIQEGTVPDNTS
CGTLPPFSSSTSPSP.TAI.S.SEHMESH.VPSSTYVPKGMNSTESNSSAS..PKV.SSIQEGTVPDNT.
RetrocopyCGTLPPFSSSTSPSPGTAIISRSEHMESHQVPSSTYVPKGMNSTESNSSASLGPKVSSSIQEGTVPDNTG
ParentalSARGKEDMNKTLPNLQVVNHQQGPHHRHILKLLPSMEATGGEKSSTPIKGSKRGHPRQNLHKHFDINEHL
SARGKEDMNKTLPNLQVVNHQQGPHHRHILKLLPS.EA.GGEKSSTP.KGSKRGHPRQNL..HFDINEH.
RetrocopySARGKEDMNKTLPNLQVVNHQQGPHHRHILKLLPSTEAPGGEKSSTPMKGSKRGHPRQNLQNHFDINEHF
ParentalPWMIVLFLLLVLVVIVVCSVRKSSRTLKKGPRQDPSAIVEKAGLKKSMTPTQNREKWIYYCNGHGIDILK
PWMIVLFLLLVLVVIVVCS..KSSRTLKKGPRQDPSA.VEK.GLKKSMT.TQNREKWIYYCNG.G.DIL.
RetrocopyPWMIVLFLLLVLVVIVVCSIQKSSRTLKKGPRQDPSATVEKVGLKKSMTRTQNREKWIYYCNGYGTDILM
ParentalLVAAQVGSQWKDIYQFLCNASEREVAAFSSGYTADHERAYAALQHWTIRGPEASLAQLISALRQHRRNDV
LVAAQVGSQWKDIYQFLCN.SEREVAAFS.G.TADHERAYAALQHW.I..PEASLAQLISALRQHRRNDV
RetrocopyLVAAQVGSQWKDIYQFLCNVSEREVAAFSNGCTADHERAYAALQHWAIQCPEASLAQLISALRQHRRNDV
ParentalVEKIRGLMEDTTQLETDKLALPMSPSPLSPSPIPSPNAKLENSTLLTVEPSPLDKNKGFFVDESEPLLRC
VEKIRGLMEDTTQLETDKLAL.MS...LSPS..PS.NAKLENSTL.TV.PSPLDKNKGFFV.ESEPLLRC
RetrocopyVEKIRGLMEDTTQLETDKLALRMSRRLLSPS--PSSNAKLENSTLRTVVPSPLDKNKGFFVGESEPLLRC
ParentalDSTSSGSSALSRNGSFITKEKKDTVLRQVRLDPCDLQPIFDDMLHILNPEELRVIEEIPQAEDKLDRLFE
..TSSGSS.L.RNGSFITKEKKDTVLRQVRLDPCDLQPIFDDMLHILNPEELRVIEEIPQAEDKLD.LFE
RetrocopyVFTSSGSSTLNRNGSFITKEKKDTVLRQVRLDPCDLQPIFDDMLHILNPEELRVIEEIPQAEDKLDQLFE
ParentalIIGVKSQEASQTLLDSVYSHLPDLL
IIGVKSQEAS.TLLDSVYSHLPDLL
RetrocopyIIGVKSQEASHTLLDSVYSHLPDLL

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 25 .25 RPM
SRP051959_heart 0 .00 RPM 14 .79 RPM
SRP051959_kidney 0 .04 RPM 83 .80 RPM
SRP051959_liver 0 .00 RPM 6 .13 RPM
SRP051959_lung 0 .03 RPM 19 .28 RPM
SRP051959_lymph_node 0 .00 RPM 7 .10 RPM
SRP051959_skeletal_muscle 0 .02 RPM 6 .53 RPM
SRP051959_spleen 0 .04 RPM 46 .81 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_4088 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4088 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4088 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Canis familiaris ENSCAFG000000020781 retrocopy
retro_cfam_10,
Callithrix jacchus ENSCJAG00000011904 1 retrocopy
retro_cjac_4088 ,


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