RetrogeneDB ID:

retro_cjac_3348

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:ACFV01170646.1:54748..57009(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FNDC3B
Ensembl ID:ENSCJAG00000002213
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3348
AAGCCTCTGCACAAAAAAACTGAAAGACTGCCAGATCGATCGCCAGAACCGCCTCAGCAGCCCTCCTTCCTCTATCTACA
AAAGCAGCTACACGACAGTGTACAATGGCTACGGGAAGGGCCACAGCGGCAGCCGTGGCGGAAGCGGCAGCGCTGGTGGT
CCCGGAATTCAGAAAACAGAGCGGGGAGCAAGAAGCAGCCCGAAGTCGAATGATTCAGACTTGCAAGAATATGAGTTGGA
AGTAAAGAGGGCGTGAGGCATTCTTTCGGGAATAGAGAAACCACAGGTTTCTAATATTCAGGCGAGAGCAGTTGTGTCGT
CCTGGGCTCCCCGCCTTGGACTTTCTTGTGGACCCCACAGTGGTCTTTCCTTCCCCTACAGTTACGAGGTTGCCTTAACA
GACAAAGGACGGGATGGAAAATACAAGATAATTTACAGTGGAGAAGAATTAGAATGTAACCTGAAAGATCTTACACCAGC
AACGGATTATCACGTGAGGGTGTCTGCCACGTACAATTCCATAAAGGGATCCTGCTCCAAGCCTGTTACCTTCACCACCC
ACAGCTGTGCACCCGAGTGTCCTATCCCTCCTAAGCTGGCCACAGGAGCAAAAGTTCACTAACCCTGCAGTGGAAGGCAC
CAGTTGACAATGGTTCAAAAATCACCAACTACCTTTTAGAGTGGGATGAGGGAAAAAGGAACAGTGGTTTCAGACAGTGC
TTCTTTGGGAGCCAGAAACACTGCAAGTTGACAAAGTTTGCCGGGCAATGGGGTACACGTTCAGGCTGGCTGCTGGAAAC
GACATTGGCACCAGTGGTTACAGCCAAGAGGTGGTGTGCTGCACATTAGGAGACATCCCTCAGATGCCTTCTGTGCCAAG
GCTGGTTCGAGCTGGCATCACATGGGTCACATTGCAGTGGAGTAAGCCAGAGGGCTGTTCACCCGAGGAGATGGTCACTT
ACACCTTGGAAATTCAGGAGGATGAAAATGATAACCCTTTCCACCCAAAATACACTGGAGAGGATTTAACCTGTACTGTG
AAAAATCTCAAAAGCAGCACACAGTATAAATTCAGGCTGACCGCTTCTACTGTGGAAGGAAGAAGCTGTCCAAGCGAAGT
CCTTGTTTGTATGACAAGTCCTGACAGGCCCGGACCTCCTACCAGACCACTTGTCAAAGGCCCAGTTACATCTCATGGCT
TTAGTGTCAAATGGGATCCTCCTAAGGACAATGGTGGATCGGAAATCCTCAAGTACTTGCTAGAGATTACTGATGGAAAT
TCTGAAGCGAATCAGTGGGAAGTGTCGTCCAGTGGGTCAGCTACCGAATATACCTTCACCCACTTGAAACCAGGCACTTT
GTACAAACTCCGAGCATGCTCTATCAGTACTGGCGGACACAGTCAGTGTTCTGAAAGTCTCCCTGTTCACACACTAAGCA
TCGAACCAGGTCAGTGTTGACCACCGAGGGTGCTGGGTAGACCGAAGCACAAAGAAGTCCACTGAGAGTGGGATGTTCCT
GCATCTGAAAGTGGCTGTGAGGTCTCAGAGTACAGCGTGGAGATGACGGAGCCTGAAGACGTAGCCTCTGAGGTGTACCA
CGGCCCAGAGCTGGAGTGCACCGTTGGCAACCTGCTTCCCGGAACCGTGTATCGCTTCAGGGTCAGGACTCTGAATGACG
GAGGGTATGGTCCCTATTCTGAGCTCTCAGAAATTACCGCTGCTGCAGGACCCCCTGGACAGTGCAAAGCACCATGTATT
TCCTTTACACCTGATGGATGTGTCTTAGTGACCTGGGAGAGTCCTGATAGTTCCAGTGCTGACATCTCAGAGTACAGGTT
GGAATGGGGAGAAGATGAAGAATCCTTAGAAGTCATTTATCATGGGACAGACACCCATTTTGAAATAAGAGACCTGTTGC
CTGCTGCACAATATTGCTGTAGACTACAGGCCTTCAATCAAGCAGGAGCAGGGCCGTACAGTGAACTTGTCCTCTGCCAG
ACACCAGCGTCTCCCCCTGACCCTGTCTGCACTCTCTGCATCCTGGAGGAGGAGCCCCTCAATGCCCACCCTGATTCACC
TTCTGTGTGCCTTGTACTGAACTGGGAAGAGCCGTGCAATAACGGATCTGAAATCCTTGCTTACAACATTGATCTTGGAG
ACACTAGCAGTACCGTGGGCAACACCACCTCCCACGTTATGAAAGATCTCCTTCCAGAAACCACCCACCGGATCAGAATT
CAGGCTATAAATGAAATTGGA

ORF - retro_cjac_3348 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.07 %
Parental protein coverage: 67.5 %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalKPPHKK-LKDRQIDRQNRLNSPPSSIYKSSCTTVYNGYGKGHSGGSGGGGSGGGPGIKKAERRARSSPKS
KP.HKK.LKD.QIDRQNRL.SPPSSIYKSS.TTVYNGYGKGHSG..GG.GS.GGPGI.K.ER.ARSSPKS
RetrocopyKPLHKK>LKDCQIDRQNRLSSPPSSIYKSSYTTVYNGYGKGHSGSRGGSGSAGGPGIQKTERGARSSPKS
ParentalNDPDLQEYELEVKRVQDILSGIEKPQVSNIQARAVVLSWAPPVGLSCGPHSGLSFPYSYEVALSDKGRDG
ND.DLQEYELEVKR...ILSGIEKPQVSNIQARAVV.SWAP..GLSCGPHSGLSFPYSYEVAL.DKGRDG
RetrocopyNDSDLQEYELEVKRA*GILSGIEKPQVSNIQARAVVSSWAPRLGLSCGPHSGLSFPYSYEVALTDKGRDG
ParentalKYKIIYSGEELECNLKDLRPATDYHVRVYAMYNSVKGSCSEPVSFTTHSCAPECPFPPKLA-HRSKSSLT
KYKIIYSGEELECNLKDL.PATDYHVRV.A.YNS.KGSCS.PV.FTTHSCAPECP.PPKLA.HRSKSSLT
RetrocopyKYKIIYSGEELECNLKDLTPATDYHVRVSATYNSIKGSCSKPVTFTTHSCAPECPIPPKLA<HRSKSSLT
ParentalLQWKAPIDNGSKITNYLLEWDEGKRNSGFRQCFFGSQKHCKLTK-LCPAMGYTFRLAARNDIGTSGYSQE
LQWKAP.DNGSKITNYLLEWDEGKRNSGFRQCFFGSQKHCKLTK..C.AMGYTFRLAA.NDIGTSGYSQE
RetrocopyLQWKAPVDNGSKITNYLLEWDEGKRNSGFRQCFFGSQKHCKLTK<VCRAMGYTFRLAAGNDIGTSGYSQE
ParentalVVCYTLGNIPQMPSAPRLVRAGITWVTLQWSKPEGCSPEEVITYTLEIQEDENDNLFHPKYTGEDLTCTV
VVC.TLG.IPQMPS.PRLVRAGITWVTLQWSKPEGCSPEE..TYTLEIQEDENDN.FHPKYTGEDLTCTV
RetrocopyVVCCTLGDIPQMPSVPRLVRAGITWVTLQWSKPEGCSPEEMVTYTLEIQEDENDNPFHPKYTGEDLTCTV
ParentalKNLKRSTQYKFRLTASNMEGKSCPSEVLVCTTSPDRPGPPTRPLVKGPVTSHGFSVKWDPPKDNGGSEIL
KNLK.STQYKFRLTAS..EG.SCPSEVLVC.TSPDRPGPPTRPLVKGPVTSHGFSVKWDPPKDNGGSEIL
RetrocopyKNLKSSTQYKFRLTASTVEGRSCPSEVLVCMTSPDRPGPPTRPLVKGPVTSHGFSVKWDPPKDNGGSEIL
ParentalKYLLEITDGNSEANQWEVSYSGSATEYTFTHLKPGTLYKLRACCISTGGHSQCSESLPVRTLSIAPGQCR
KYLLEITDGNSEANQWEVS.SGSATEYTFTHLKPGTLYKLRAC.ISTGGHSQCSESLPV.TLSI.PGQC.
RetrocopyKYLLEITDGNSEANQWEVSSSGSATEYTFTHLKPGTLYKLRACSISTGGHSQCSESLPVHTLSIEPGQC*
ParentalPPRVLGRPKHKEVHLEWDVPASESGCEVSEYSVEMTEPEDVASEVYHGPELECTVGNLLPGTVYRFRVRA
PPRVLGRPKHKEVH.EWDVPASESGCEVSEYSVEMTEPEDVASEVYHGPELECTVGNLLPGTVYRFRVR.
RetrocopyPPRVLGRPKHKEVH*EWDVPASESGCEVSEYSVEMTEPEDVASEVYHGPELECTVGNLLPGTVYRFRVRT
ParentalLNDGGYGPYSDVSEITTAAGPPGQCKAPCISFTPDGCVLVNWESPDSSGADISEYRLEWGEDEESLEVIY
LNDGGYGPYS..SEIT.AAGPPGQCKAPCISFTPDGCVLV.WESPDSS.ADISEYRLEWGEDEESLEVIY
RetrocopyLNDGGYGPYSELSEITAAAGPPGQCKAPCISFTPDGCVLVTWESPDSSSADISEYRLEWGEDEESLEVIY
ParentalHGTDTHFEIRDLLPAAQYCCRLQAFNQAGAGPYSELVLCQTPASPPDPVCTLCVLEEEPLNAHPDSPSAC
HGTDTHFEIRDLLPAAQYCCRLQAFNQAGAGPYSELVLCQTPASPPDPVCTLC.LEEEPLNAHPDSPS.C
RetrocopyHGTDTHFEIRDLLPAAQYCCRLQAFNQAGAGPYSELVLCQTPASPPDPVCTLCILEEEPLNAHPDSPSVC
ParentalLVLNWEEPCNNGSEILAYNIDLGDTSITVGNTTSHVMKDLLPETTYRIRIQAINEIG
LVLNWEEPCNNGSEILAYNIDLGDTS.TVGNTTSHVMKDLLPETT.RIRIQAINEIG
RetrocopyLVLNWEEPCNNGSEILAYNIDLGDTSSTVGNTTSHVMKDLLPETTHRIRIQAINEIG

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 .82 RPM 54 .45 RPM
SRP051959_heart 1 .93 RPM 49 .18 RPM
SRP051959_kidney 0 .98 RPM 39 .45 RPM
SRP051959_liver 2 .99 RPM 33 .75 RPM
SRP051959_lung 3 .77 RPM 40 .33 RPM
SRP051959_lymph_node 6 .60 RPM 21 .73 RPM
SRP051959_skeletal_muscle 1 .53 RPM 18 .58 RPM
SRP051959_spleen 2 .52 RPM 53 .97 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_3348 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3348 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3348 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 ENSCJAG00000002213 1 retrocopy
retro_cjac_3348 ,


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