RetrogeneDB ID:

retro_cjac_2512

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:5:32558512..32559942(+)
Located in intron of:ENSCJAG00000011302
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PRAME
Ensembl ID:ENSCJAG00000020319
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2512
GAGAGCCTGCTGAAGAATGAGGCCCTGGCCATCGCTGTCTTGGAGTTGCTCCCCAAAATTTTTTCCCGCCACTCTTCAGG
GCAGACTTTGACGGGAAACACAACCAGACTCTGAAGGCAATGGTGCAGGCCTGGCCCTTCACCTGCCTCCCTCTGGGAGT
GCTGATGAAGGGACAGCAGCTTCACGTGGAAACCTTCAAAGCTGTGCTTGAAGGAGTTGATGTGCTGCTTGCCCAGGAGG
TTCACCCCAGGAGGTGGACACTCAAAGTGCTGGATGTAGGAAAGCATTCTCATCAAGACTTCTGGACCATATGGTCTGGA
AAAAGGGTCAGTCTGCTCATTTCCAGAGCCAGAAGCAGCTCAGCCCATGAGAAAGAAGCGAAAATAGATGGTTTGAGCAC
AGAAGCAGAGAAGCCCTTTACTCCAAAAGATGTTCTCGTAGACCTGTCCCTCAAGGAAGGTGCCTATGATGAATTGTTCA
CCCACCTGATTGAGATAGTGAGGCGAAAGAAAGATGTACTACACCTGTGCTGTAAGAAGCTGAAGATTTTTTGCCATGCC
TGTGCAGAATATCAAGATGATCCTGAAAATGGTGCAGCTGGACTCTATTGAAGATTTGGAAGTGACTTGCACCTGGAAAC
TAACCTCCTTGGTGAAATTTTCTCCTCACCTGAGCCAGATAAGTAATCTATGTAGACTACTCCTCGCTCACATCCATCCA
TCTTCCTTCATTTCCCCAGAGAAGGAGGAGCAGTATATCGCCCAGTTCACCTCTCAGTTCCTCAGTCTCCACTGCCTCCA
GGAGCTCTACATGGACTCTTTATTTTTCCTCTGAGGCCGCCTGGATCAGTTGCTCAGATGCATGATGAACCCCTTGGAAA
CCCTTTCGATAACTAACTGCTGGCTTTCAGAAGAAGATGTGACACATCTGTCCTGGAGCCCCAGCATCAGTCAGCTGAGT
GTCTTGAGTCTAAGTGGGGTCATGCTGACCGAGATAAATCCCGAGCTCCTCCAAGCTCTGCTAGAGAGAACCTCCGCCAC
CCTCCAGGACCTGGACTTAGATGAGTGTGGGATCATGGATACTCAGCTCCTTATTCTTCTGCCTTCCCTGAGCCACTGCT
CCCAGCTTACCACCTTCAGCTTCTGCAGGAATCCCATCTCCATGTCTGTCCTGGAGAACCTCGTGCACCACATCATCGGA
TTGAATAATCTGAGCCACTTGCTGTATCCTGTCCGCATGGAGAGTTAGGAGGACGTCAATGGCACCCTCGACCTGGGGAG
ACTTGCCTATCTGCACACCAGGCTAGGGAGTTGCTGTGTGAATTGGGGTGGCCTGGCATGGTCTGGCTCAGTGCCAACTC
CTGTCCTCACTGTGGGGACAGAACCTTCTATGACCCAGATCCCATCCTGTGCCCCTGTTTCACGCCTGCC

ORF - retro_cjac_2512 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.03 %
Parental protein coverage: 93.91 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalQSLLKNESLAIAALELLPR-ELFPPLFTAAFDGRHNKTLKAMVQAWPFTCLPLGVLMKGQQLHVETFKAV
.SLLKNE.LAIA.LELLP....FPPLF.A.FDG.HN.TLKAMVQAWPFTCLPLGVLMKGQQLHVETFKAV
RetrocopyESLLKNEALAIAVLELLPK<NFFPPLFRADFDGKHNQTLKAMVQAWPFTCLPLGVLMKGQQLHVETFKAV
ParentalLDGVDVLLAQEVRPRRWKLKVLDLRKNSHQDFWTVWSGKRVSLCSFPEPEAAQPMRKKRKVDGSSTEAEQ
L.GVDVLLAQEV.PRRW.LKVLD..K.SHQDFWT.WSGKRVSL.............K..K.DG.STEAE.
RetrocopyLEGVDVLLAQEVHPRRWTLKVLDVGKHSHQDFWTIWSGKRVSLL-ISRARSSSAHEKEAKIDGLSTEAEK
ParentalRFIPIEVLVDLSLKEGAYDELFIHLIEIVRRKKDVLHLCCKKLKI-FAMPVQNIKMILKMVQLDSIEDLE
.F.P..VLVDLSLKEGAYDELF.HLIEIVRRKKDVLHLCCKKLKI.FAMPVQNIKMILKMVQLDSIEDLE
RetrocopyPFTPKDVLVDLSLKEGAYDELFTHLIEIVRRKKDVLHLCCKKLKI>FAMPVQNIKMILKMVQLDSIEDLE
ParentalVTCTWKLPTLAKFSPHLSQMSNLRRLLLAHIHPASFISPEKEEQFIAQFISQFLNLHCLEELYVDSLFFL
VTCTWKL..L.KFSPHLSQ.SNL.RLLLAHIHP.SFISPEKEEQ.IAQF.SQFL.LHCL.ELY.DSLFFL
RetrocopyVTCTWKLTSLVKFSPHLSQISNLCRLLLAHIHPSSFISPEKEEQYIAQFTSQFLSLHCLQELYMDSLFFL
ParentalRGHLDQLLRCMMNPLETLSITNCWLSEEDVTHLSQSPNISQLSVLSLSGVMLTEINPELLQALLERTSAT
.G.LDQLLRCMMNPLETLSITNCWLSEEDVTHLS.SP.ISQLSVLSLSGVMLTEINPELLQALLERTSAT
Retrocopy*GRLDQLLRCMMNPLETLSITNCWLSEEDVTHLSWSPSISQLSVLSLSGVMLTEINPELLQALLERTSAT
ParentalLQDLDLDECGIVDTQLLVLLPSLSHCSQLTTFSFCGNPISISVLESLVHHIIGLNNLSHVLYPVPVESFE
LQDLDLDECGI.DTQLL.LLPSLSHCSQLTTFSFC.NPIS.SVLE.LVHHIIGLNNLSH.LYPV..ES.E
RetrocopyLQDLDLDECGIMDTQLLILLPSLSHCSQLTTFSFCRNPISMSVLENLVHHIIGLNNLSHLLYPVRMES*E
ParentalDINGTLDLGRLAYLHTRL-RELLCELGRPGMVWLSATPCPHCGDRTFYDPDPILCPCFMPA
D.NGTLDLGRLAYLHTRL.RELLCELG.PGMVWLSA..CPHCGDRTFYDPDPILCPCF.PA
RetrocopyDVNGTLDLGRLAYLHTRL<RELLCELGWPGMVWLSANSCPHCGDRTFYDPDPILCPCFTPA

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 1 .84 RPM 0 .20 RPM
SRP051959_heart 1 .26 RPM 0 .19 RPM
SRP051959_kidney 1 .06 RPM 0 .18 RPM
SRP051959_liver 0 .67 RPM 0 .26 RPM
SRP051959_lung 2 .10 RPM 0 .31 RPM
SRP051959_lymph_node 2 .44 RPM 0 .32 RPM
SRP051959_skeletal_muscle 0 .83 RPM 0 .09 RPM
SRP051959_spleen 2 .02 RPM 0 .19 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_2512 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2512 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2512 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000020319 2 retrocopies
retro_cjac_1383, retro_cjac_2512 ,


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