RetrogeneDB ID:

retro_cjac_3916

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL286236.1:41750..43304(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000007968
Aliases:None
Status:KNOWN_PSEUDOGENE
Parental gene
information
Parental gene summary:
Parental gene symbol:TCF25
Ensembl ID:ENSCJAG00000010545
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3916
GTGTCGCGCCGGGCCCTCAGGAGGCTGAGAGGGGAACAGCGCGGCCACGAGCCCCTGGGGCCAGCGCCCTGCAGTTTGAC
CTCCCTGATGACGATGACGTGGAAGAAGGGCCCAAGTGGGAGCTGGGTGGCCGGCACCTCGGGGAGGCAGGGAAGGAGGG
CGTCCGAGTCAACAACCGGTTCCAGCTGATAAACATTGAAGATCTTGAGGGTGACCCTGTGGTGAATGGGGAGAGGTCTG
GCTCTTCGCTCACAGACACTGCGGCACCGGGGAACAAAGGAAGGGCTGCCTGTGAAAACACAGACACCAAGGCGGAGGAG
GCTGGCCAGGACAGTGCCCCCGGAGCGGTCTAATGCAAGTGGCAAACTCCGGAAGAAGAAAAAGAAACAGAAAACTAAGA
AAAGCAGCACGGGAGAAGCACTGGAAAACGGACTAGAAGATATTGATCGCACCCTAGAGAGAACTGAGGACAGCGGTGGT
TTGAACCGTCCTGGCCCAACTCCCCTGAGCTCCAGGAAGCGCGTTCTCTAAGTGGAGCACAGACATTTGAATCCAGACAC
AGAACTGAAAAGGTATTTTGGTGCTCGGCCAGTCCTGGGGGAACAAAGGCCACGGCAGAGACAGCGCGTATACCCCAAGT
GACATGGCTGACGACCCCTAAGAGCACCTGGCCCCGGTACAGCAAACCAGGTCTGTCCATGCGGCTGCTGGAATCGAAAA
AACGCCTGCCCTTGTTTGAGCACAGTGAGGCGTACCAGCAGGCGCAGCACAAGTTCCTGGTGGCCGTGGAGTCCATGGAG
CCCAACAACATCGTGGTTCTGCTCCAGATAAGCCCATATCACGTGGACTCACTCCTGCAGCTCAGCGATGCCTGCCACTT
TCAAGAGGATCAGGAGATGGCTCGAGACCTCATAGAGAGAGCGCTGTACAGTATGGAGTGTGCGTTCCACCCCTTGTTCA
GCCTCACCAGCGGGGCTTGCCGGCTGGATTACCGCAGACCCGAGAACAGGAGCTTCTACCTGGCCCTCTACAAGCAGATG
AGCTTCCTGGAGAAGCGAGGCTGCCCACGCACCGCCCTGGAGTACTGCAAGCTCATCCTGAGTCTCGAGCCGGATGAGGA
CCCCCTCTGCATGCTGCTGCTCATTGACCACCTGGCCTTGCGGCCCGGAACTACGAATACCTTATCCGCCTCTTCAGGAG
TGAGAGGCTCATCGGAACCTGTCGCAGCTCCCAAATTTTGCCTTCTCTGTTCCACTGGCATATTTCCTGCTGAGCCAACA
GACAGACCTCCCTGGGCACGAGCAGAGCTCTGCCAGGGAGAAGGCCTCGCTCTTGATACAGCAGGCGCTCACCATGTTTC
CTGGAGTCCTCCTGCCCCTGCTCGAGTACTGCAGCGTGCGGCCCGATGCCACCGTGTCCACTCATCGCTTCTTTGGACCC
AATGCTGAGATAAGCCAGCCCCCTGCCCTGAGCCAGCTGGTGAGCCTGTATCTCGGGAGGTCACACTTTCTCTGGAAAGA
GCCCGCCACCATGAGCTGGCTGGAGGAGAACATC

ORF - retro_cjac_3916 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.93 %
Parental protein coverage: 77.37 %
Number of stop codons detected: 2
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMSRRALRRLRGEQRGQEPLGPG-ALQFDLRDDDDAEEEGLKRELGGRRPGEAGKEGVRVNNRFELINIED
.SRRALRRLRGEQRG.EPLGP..ALQFDL.DDDD.EE.G.K.ELGGR..GEAGKEGVRVNNRF.LINIED
RetrocopyVSRRALRRLRGEQRGHEPLGPA<ALQFDLPDDDDVEE-GPKWELGGRHLGEAGKEGVRVNNRFQLINIED
ParentalLEDDPVVNGERSGSSLTDTAAPGNKGRAPCGNTDTKAD-GG-VARTAPPEQSNASGKLRKKKKKQKAKKS
LE.DPVVNGERSGSSLTDTAAPGNKGRA.C.NTDTKA..GG..ART.PPE.SNASGKLRKKKKKQK.KKS
RetrocopyLEGDPVVNGERSGSSLTDTAAPGNKGRAACENTDTKAE<GG<LARTVPPERSNASGKLRKKKKKQKTKKS
ParentalSTGEAVENGLEDIDRILERIEDSSGLNRPGPAPLSSRKHILYVEHRHLNPDTELKRYFGARAVLGEQRPR
STGEA.ENGLEDIDR.LER.EDS.GLNRPGP.PLSSRK..L.VEHRHLNPDTELKRYFGAR.VLGEQRPR
RetrocopySTGEALENGLEDIDRTLERTEDSGGLNRPGPTPLSSRKRVL*VEHRHLNPDTELKRYFGARPVLGEQRPR
ParentalQRQRVYPK-CTWLTTPKSTWPRYSKPGLSMRLLESKKGLSLFAFEHSEEYQQAQHKFLVAVESMEPNNIV
QRQRVYPK..TWLTTPKSTWPRYSKPGLSMRLLESKK.L.LF..EHSE.YQQAQHKFLVAVESMEPNNIV
RetrocopyQRQRVYPK<VTWLTTPKSTWPRYSKPGLSMRLLESKKRLPLF--EHSEAYQQAQHKFLVAVESMEPNNIV
ParentalVLLQTSPYHVDSLLQLSDACRFQEDQEMARDLIERALYSMECAFHPLFSLTSGACRLDYRRPENRSFYLA
VLLQ.SPYHVDSLLQLSDAC.FQEDQEMARDLIERALYSMECAFHPLFSLTSGACRLDYRRPENRSFYLA
RetrocopyVLLQISPYHVDSLLQLSDACHFQEDQEMARDLIERALYSMECAFHPLFSLTSGACRLDYRRPENRSFYLA
ParentalLYKQMSFLEKRGCPRTALEYCKLILSLEPDEDPLCMLLLIDHLALR-ARNYEYLIRLF-QEWEAHRNLSQ
LYKQMSFLEKRGCPRTALEYCKLILSLEPDEDPLCMLLLIDHLALR.ARNYEYLIRLF.QE.EAHRNLSQ
RetrocopyLYKQMSFLEKRGCPRTALEYCKLILSLEPDEDPLCMLLLIDHLALR<ARNYEYLIRLF<QE*EAHRNLSQ
ParentalLPNFAFSVPLAYFLLSQQTDLPEHEQSSAREKASLWIQQALTMFPGVLLPLLEYCSVRPDATVSTHPFFG
LPNFAFSVPLAYFLLSQQTDLP.HEQSSAREKASL.IQQALTMFPGVLLPLLEYCSVRPDATVSTH.FFG
RetrocopyLPNFAFSVPLAYFLLSQQTDLPGHEQSSAREKASLLIQQALTMFPGVLLPLLEYCSVRPDATVSTHRFFG
ParentalPNAEISQPPALSQLVSLYLGRSHFLWKEPTTMSWLEENV
PNAEISQPPALSQLVSLYLGRSHFLWKEP.TMSWLEEN.
RetrocopyPNAEISQPPALSQLVSLYLGRSHFLWKEPATMSWLEENI

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 2 .09 RPM 24 .56 RPM
SRP051959_heart 1 .53 RPM 24 .50 RPM
SRP051959_kidney 1 .04 RPM 30 .97 RPM
SRP051959_liver 1 .41 RPM 28 .79 RPM
SRP051959_lung 3 .37 RPM 24 .99 RPM
SRP051959_lymph_node 5 .11 RPM 29 .27 RPM
SRP051959_skeletal_muscle 1 .55 RPM 20 .09 RPM
SRP051959_spleen 1 .45 RPM 27 .88 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_3916 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3916 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3916 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 ENSCJAG00000010545 1 retrocopy
retro_cjac_3916 ,


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