RetrogeneDB ID:

retro_cjac_2442

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:4:54981734..54983880(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:FTSJD2
Ensembl ID:ENSCJAG00000005567
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2442
CCCCCATCAACAAACAAAAAAAGAGTTGCAGAGCTTGCCCTGAGCCTCAGCTCCACGTCCAATGACGAACCTCCTTCCTC
TGTCAATCATGGAGCAAAAGCATCTGCTACAAGCCTTAGTGGGTCTGACAGTGATTCCGAGGGGAAACAACGCAGCTCTG
ACTCTTTTGATGATGCAGTCAAAGCAGACTCCCTTGTGGAGGGAACTTCTTCTCGCTACTCCATGTATAATAGTGTCTCC
CAGAAGCTTATGGCCAAGATGGGCTTCAGGGAAGGTGAAGGAATGGGCAAATACGACCAGGGTTGGAAGGACATCGTTGA
GACTTCCAATCAGAAAGGTCAACGAGACTTGGGTCTGACACTCCAGGGCTTTGACCAGATGCTGAACATGGACTGGTGAG
ATGATCCAGAACCCCGTGCCTGTGAGCAGGTGTCATGGTTCCCTGAATGTACCACTGAAATTCCTGACACTAAGGAAATG
AATGATTGGATGGTTGTAGAAAAGAGAAAGATGATTATTGAAGATGAAACAGAGTTTTGTGGGGAAGAGCTCTTCATAGT
GTTGCAGTGTAAGAGCATGTTGGATGTCCTGGATGGGGAAGAGATGCGGCAAGCTCAGACTCGGGCCAATCCCTACGAGA
TGATCCGAGGAGTCTTCTTTCTAAACAGGGCAGCAATGAAGATGGCTAACATGGATTTTGTGTTTGATTGCATGTTCACA
AATCTGAGGGACTCTTATGGGAAGCCACTGGTGAAGGACTGGGAAGCTGAGCTTCTGTACTTTGCTGATGTCTGCGCAGG
CCCAGGAGGCTTCTGAGAGTATGTGCTGTGGTGGAAGAAGTGGCATGCAAAGGGCTTTGGAATGACTTGGAAGGGCCCTA
ATGACTTCAAGCTGGAGGACTTCTACTCTGCCTCCAGTGAACTCTCTGAACCCTACTATGGTGAAGGTGGGATTGATGGA
GATGGAGATATCACCCGCCCAGAGAAAACATCTCTGCTTTTCAGAATTTTGTCCTGGATAACACAGATCGCAAGGGTGTC
CACTTTCTGATGGCCGATGGGGGTTTCTTAGTGGAGGGACAGGAGAACCTACAGGAGATCCTCAGCAAGCAGCTCCTGCT
GTGTCAGTTCCTCATGGCGCTGTCCATTGTCCGGACAGGAGGCCACTTCATCTGTAAAACCTTTGACCTTTTCACACCAT
TCAGTGTGGGGCTTGTCTACCTGCTGTACTGCTGCTTTGAACGAGTTTGTCTCTTCAAGCCTATTACCAGCCGTCCTGCC
AACTCAGAGAGGTACATGGTGTGCAAGGGCCTGAAGGTGGGCATAGATGACATTCAGGATTACCTCTTCGCAGTAAATAT
TAAACTCAATCAGCTGCAGAACACTGATTCTGACGTCAACTTGGTGGTCCCGCTGGAGGTGATCAAGGGAGACCATGAAT
TTACTGACTGCATGATATGGACCAAGGAGAGCCACTGTAGTCTACAAATTAAAGCTCTGGTGAAAAATTATGTCTTTGTT
CAAGACATGACACTAAGTGAGCCTCGGCAAGCAGAGATCCGGAAGGAGTGCCTCCGACTCTGGGGGATCCCAGACCAGGC
TCGTGCGGCTCCTTCCTCAGACCCCAAATCAAAGTTCTTTGAGCTGATCCAGGGTACTGAGATTGACATCTTCAGCTACA
AGCCCACACTGCTCACCTCTAAAACCCTGGAGAAGATCTGCCCTGTGTTTGACTACTGCTGCATGGTGTCTGGCAGTGAG
CAGAAGTTCCTCATTGGCCTAGGGAAATCCCAGATCTACACGTGGGATGGCTGCCAGTCAGACCACTGGGTCAAGCTAAA
CCTGAAGACAGAGCTGCCCTGGGACACTCTGCTGTCTGTGGAAATTGTACATGAGCTGAAAAGGGAGGGGAAGGCCCAGC
GGAAGATCAGTGCCATCTATATCCTTGATGTCCTTGTGCTGAATGGCACCGATCTCTGGGAGCAGCATTTTAACTGTGAA
TTCAGCTTGCTGAGAAATTTGTGAAAGCCGTTTCGAAGCCTAGTTGGCCTGACATGAATTGCATCAGGGTGAAGAAGGTG
TAAAGACTGGAAGAGATGGAGAAGATTTTTGTCAGGTTGGAGATGAAGATCATCAAGGGCTCCAGT

ORF - retro_cjac_2442 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 89.72 %
Parental protein coverage: 85.87 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPIKKQKKRVAELALSLSSTSDDEPPSSVNHGAKASATSLSGSDSETEGKQRSSDSFDDAFKADSLVEGTS
P....KKRVAELALSLSSTS.DEPPSSVNHGAKASATSLSGSDS..EGKQRSSDSFDDA.KADSLVEGTS
RetrocopyPPSTNKKRVAELALSLSSTSNDEPPSSVNHGAKASATSLSGSDSDSEGKQRSSDSFDDAVKADSLVEGTS
ParentalSRYSMYNSVSQKLMAKMGFREGEGLGKYSQGRKDIVEASNQKGRRGLGLTLRGFDQELNVDWRDEPEPSA
SRYSMYNSVSQKLMAKMGFREGEG.GKY.QG.KDIVE.SNQKG.R.LGLTL.GFDQ.LN.DW.D.PEP.A
RetrocopySRYSMYNSVSQKLMAKMGFREGEGMGKYDQGWKDIVETSNQKGQRDLGLTLQGFDQMLNMDW*DDPEPRA
ParentalCEQVSWFPECTTEIPDTKEMSDWMVVGKRKMIIEDETEFCGEELLHSVLQCKSVFDVLDGEEMRRARTRA
CEQVSWFPECTTEIPDTKEM.DWMVV.KRKMIIEDETEFCGEEL...VLQCKS..DVLDGEEMR.A.TRA
RetrocopyCEQVSWFPECTTEIPDTKEMNDWMVVEKRKMIIEDETEFCGEELF-IVLQCKSMLDVLDGEEMRQAQTRA
ParentalNPYEMIRGVFFLNRAAMKMANMDFVFDRMFTNPRDSYGKPLVKDREAELLYFADVCAGPGGFSEYVLWRK
NPYEMIRGVFFLNRAAMKMANMDFVFD.MFTN.RDSYGKPLVKD.EAELLYFADVCAGPGGF.EYVLW.K
RetrocopyNPYEMIRGVFFLNRAAMKMANMDFVFDCMFTNLRDSYGKPLVKDWEAELLYFADVCAGPGGF*EYVLWWK
ParentalKWHAKGFGMTLKGPNDFKLEDFYSASSELFEPYYGEGGIDGDGDITRPENIS-AFR-NFVLDNTDRKGVH
KWHAKGFGMT.KGPNDFKLEDFYSASSEL.EPYYGEGGIDGDGDITRPE..S..FR.NFVLDNTDRKGVH
RetrocopyKWHAKGFGMTWKGPNDFKLEDFYSASSELSEPYYGEGGIDGDGDITRPEKTSLLFR<NFVLDNTDRKGVH
ParentalFLMADGGFSVEGQENLQEILSKQLLLCQFLMALSIVRTGGHFICKTFDLFTPFSVGLVYLLYCCFERVCL
FLMADGGF.VEGQENLQEILSKQLLLCQFLMALSIVRTGGHFICKTFDLFTPFSVGLVYLLYCCFERVCL
RetrocopyFLMADGGFLVEGQENLQEILSKQLLLCQFLMALSIVRTGGHFICKTFDLFTPFSVGLVYLLYCCFERVCL
ParentalFKPITSRPANSERYVVCKGLKVGIDDVRDYLFAVNIKLNQLRNTDSDVNLVVPLEVIKGDHEFTDYMIRS
FKPITSRPANSERY.VCKGLKVGIDD..DYLFAVNIKLNQL.NTDSDVNLVVPLEVIKGDHEFTD.MI..
RetrocopyFKPITSRPANSERYMVCKGLKVGIDDIQDYLFAVNIKLNQLQNTDSDVNLVVPLEVIKGDHEFTDCMIWT
ParentalNESHCSLQIKALAKIHAFVQDTTLSEPRQAEIRKECLRLWGIPDQARVAPSSSDPKSKFFELIQGTEIDI
.ESHCSLQIKAL.K...FVQD.TLSEPRQAEIRKECLRLWGIPDQAR.AP.SSDPKSKFFELIQGTEIDI
RetrocopyKESHCSLQIKALVKNYVFVQDMTLSEPRQAEIRKECLRLWGIPDQARAAP-SSDPKSKFFELIQGTEIDI
ParentalFSYKPTLLTSKTLEKIRPVFDYRCMVSGSEQKFLIGLGKSQIYTWDGRQSDRWVKLDLKTELPRDTLLSV
FSYKPTLLTSKTLEKI.PVFDY.CMVSGSEQKFLIGLGKSQIYTWDG.QSD.WVKL.LKTELP.DTLLSV
RetrocopyFSYKPTLLTSKTLEKICPVFDYCCMVSGSEQKFLIGLGKSQIYTWDGCQSDHWVKLNLKTELPWDTLLSV
ParentalEIVHELKGEGKAQRKISAIHILDVLVLNGTDVREQHFNQR-IQLAEKFVKAVSKPSRPDMNPIRVKEVYR
EIVHELK.EGKAQRKISAI.ILDVLVLNGTD..EQHFN...IQLAEKFVKAVSKPS.PDMN.IRVK.V.R
RetrocopyEIVHELKREGKAQRKISAIYILDVLVLNGTDLWEQHFNCE<IQLAEKFVKAVSKPSWPDMNCIRVKKV*R
ParentalLEEMEKIFVRLEMKIIKGSS
LEEMEKIFVRLEMKIIKGSS
RetrocopyLEEMEKIFVRLEMKIIKGSS

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 .42 RPM 21 .46 RPM
SRP051959_heart 0 .96 RPM 22 .78 RPM
SRP051959_kidney 0 .58 RPM 24 .16 RPM
SRP051959_liver 0 .17 RPM 17 .78 RPM
SRP051959_lung 1 .09 RPM 24 .74 RPM
SRP051959_lymph_node 1 .42 RPM 24 .09 RPM
SRP051959_skeletal_muscle 0 .13 RPM 25 .09 RPM
SRP051959_spleen 0 .63 RPM 24 .79 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_2442 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2442 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2442 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 ENSCJAG00000005567 1 retrocopy
retro_cjac_2442 ,


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