RetrogeneDB ID:

retro_cjac_2769

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:6:125287822..125289435(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DVL3
Ensembl ID:ENSCJAG00000013060
Aliases:None
Description:dishevelled segment polarity protein 3 [Source:HGNC Symbol;Acc:3087]


Retrocopy-Parental alignment summary:






>retro_cjac_2769
GACCTGCCTCCGCCTCTTGAGCGGACAGGTGGCATCGGGGACTCCCGGCCCCCCTCCTTCCACCCGAATGTGGCCAGCAG
CCGTGGCGGGATGGACAATGAGACGGGCACGGAGTCCATGGTCAGCCACCGAGGGGAGCGTGCCCGCCGCCGGAACCACA
AGGAGGCTGCCCGGACCAATGGGTACCCGAGGGGAGACCGGCGGCGGGACGTGGGGCTGCCCCCAGACAGCACGTCCACT
GCCCTGAGCAGCGAGCTCGAGTCCAGCAGCTTTGTGGACTCAGATGAGGATGGCAGCACGAGCTGGCTGAGCAGCTCCAC
CGAGCAGAGCAAGTCATCCAGGCTCATCCGGAAGCACAAGCTCCGGTGGAGGAAGCAGCGCCTGCGGCAGACGGACCGGG
CCTCCTCCTTCAGCAGCATTACGGACTCCACCATGTCTCTCAACATCGTCACCGTCACGCTCAACATTGAGAGACACCAC
TTCCTTGGCATCAGCATCGTGGGGCAGAGCAACGATCGCGGAGATGGCGGCATTTACATAGGTTCCATAATGAAGGGCGG
AACAGTGGCCGCTGATGGTCGAATTGAGCCCGGGGACATGCTGCTGCAGGTAAATGATGTGAACTTTGAGAACATGAGCA
ACGACGACGCTGTGCGGGTTCTTCGGGAGATTGTGTCCCAGACAGGACCCATCAGTCTTACCGTGGCCAAGTGCTGGGAC
CCAACAGCCAGAAACTACTTCACCGTCCCAAGGGCTGACCCGGTGTGGCCCCTCGACCCTGCTGCCTGGCTGTCCCACAG
GGCGGCACTGACAGGAGCCCTGCCCCGCTACAGTAGGAGCCCCCTTCTCCAGCACCGTCATGCGCACCAGCTCCTCCTCA
CTAACCAGCTCCGTGCCTGGCGCTCCACAGCTGGAGGAGGCGCCGCTGACGGTGAAGAGTGACATGGGCGCTGACGTCTG
GGTCATGCAGCTGCCGGACTCGGGACTGGAGATTCGTGACCGCATGTCCCTCAAGATCACCATCGCCACACCGTCATCGG
AGCGGACGTGGTGGACTGGCTGTACACGCACGTGGAGGGCTTCAAGGAGCGTTGGGAGGCCTGGAAGTACGCCAGCAGCT
TGCTGAAGCACGGCTTCCTGCGGCACACGGTCAACAAGATCACCTTCTCCTAGCAGTGCTACTACGTCTTCGGGGACCTG
TGTAGCAATCTCACGGCCCTGAACCTCAACAGTGGCTCCAGCGGGGCCTCGGATCGGGACACGCTGGCCCCGATGCCCCA
CCCGACCACCACCCCCTGGCCCCTGGGTCAGGGCTACCCCTACCAGTACCTGGGACTCCCGCCCTGCTTCCCACCTGCCT
ACCAGGACCCGGGCTTTAGCTATGGCAGCGGCAGCACTGGGAGACAGCAGAGTGAAGGGAGCAAGAGTAGCGGGTCTGCC
CGGAGCAGCCGCCGGGCACTGGGCCGTGAGAAGGAGCGTAGCGTCGGGTGGCATGAGCTGGGGGCAGCGGCAGCGAATCG
GACCACACGGCACCGAGTGGGGTGGGCAGCAGGTGGCGGGAGTGTCCAGCTGGCCAGCTCAGCCGAGGAATAAGCCCACG
CAGTCAGGCTTCA

ORF - retro_cjac_2769 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 61.24 %
Parental protein coverage: 81.17 %
Number of stop codons detected: 1
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalELPPPMERTGGIGDSRPPSFHPHAGGGSQENLDNDTETDSLVSAQRERPRRRDGPEHAARLNGTAKGERR
.LPPP.ERTGGIGDSRPPSFHP.....S....DN.T.T.S.VS...ER.RRR...E.AAR.NG...G.RR
RetrocopyDLPPPLERTGGIGDSRPPSFHPNVAS-SRGGMDNETGTESMVSHRGERARRRNHKE-AARTNGYPRGDRR
ParentalREPG-GYDSSPTLMSSELETTSFCDSDEDDSTSRFSSSTEQSSASRLMRRHKRRRRKQKVSRIERXSSFS
R..G...DS..T..SSELE..SF.DSDED.STS..SSSTEQS..SRL.R.HK.R.RKQ......R.SSFS
RetrocopyRDVGLPPDSTSTALSSELESSSFVDSDEDGSTSWLSSSTEQSKSSRLIRKHKLRWRKQRLRQTDRASSFS
ParentalSITDSTMSLNIITVTLNMEKYNFLGISIVGQSNERGDGGIYIGSIMKGGAVAADGRIEPGDMLLQVNEIN
SITDSTMSLNI.TVTLN.E...FLGISIVGQSN.RGDGGIYIGSIMKGG.VAADGRIEPGDMLLQVN..N
RetrocopySITDSTMSLNIVTVTLNIERHHFLGISIVGQSNDRGDGGIYIGSIMKGGTVAADGRIEPGDMLLQVNDVN
ParentalFENMSNDDAVRVLREIVHKPGPITLTVAKCWDPSPRGCFTLPRSEPIRPIDPAAWVSHTAAMTGTFPAYG
FENMSNDDAVRVLREIV...GPI.LTVAKCWDP..R..FT.PR..P..P.DPAAW.SH.AA.TG..P.Y.
RetrocopyFENMSNDDAVRVLREIVSQTGPISLTVAKCWDPTARNYFTVPRADPVWPLDPAAWLSHRAALTGALPRYS
ParentalMSPSL-STITST-SSSITSSIPDTERLDDFHLSIHSDMAAIVKAMASPESGFEVRERMWLKITIP-NAFI
.SP.L.ST...T.SSS.TSS.P....L....L...SDM.A.V..M..P.SG.E.R.RM.LKITI.....I
RetrocopyRSPLL>STVMRTSSSSLTSSVPGAPQLEEAPLTVKSDMGADVWVMQLPDSGLEIRDRMSLKITIA<HTVI
ParentalGSDVVDWLYHNVEGFTDRREARKYASNLLKAGFIRHTVNKITFSEQCYYIFGDLCGNMANLSLHDHDGSS
G.DVVDWLY..VEGF..R.EA.KYAS.LLK.GF.RHTVNKITFS.QCYY.FGDLC.N...L.L....GSS
RetrocopyGADVVDWLYTHVEGFKERWEAWKYASSLLKHGFLRHTVNKITFS*QCYYVFGDLCSNLTALNL--NSGSS
ParentalGASDQDTLAPLPHPGAAPWPM--AFPYQYPPPPHPYNPHPGFPELGYSYGGGSASSQHSEGSRSSGSNRS
GASD.DTLAP.PHP...PWP.....PYQY...P.P..P.P.....G.SYG.GS...Q.SEGS.SSGS.RS
RetrocopyGASDRDTLAPMPHPTTTPWPLGQGYPYQYLGLP-PCFP-PAYQDPGFSYGSGSTGRQQSEGSKSSGSARS
ParentalGSDR-RKEKDPKAGDSK-SGGSGSESDHTTRSSLRGPRERAPSERSGPAASEHSHRS
.......EK....G.....GGSGSESDHT..S.........P........S..S..S
RetrocopySRRALGREKERSVGWHE<AGGSGSESDHTAPSGVGSRWRECPAGQLSRGISPRSQAS

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 .73 RPM 12 .29 RPM
SRP051959_heart 1 .47 RPM 19 .15 RPM
SRP051959_kidney 2 .15 RPM 16 .93 RPM
SRP051959_liver 1 .36 RPM 5 .68 RPM
SRP051959_lung 1 .35 RPM 12 .82 RPM
SRP051959_lymph_node 0 .55 RPM 8 .86 RPM
SRP051959_skeletal_muscle 2 .27 RPM 11 .14 RPM
SRP051959_spleen 0 .53 RPM 12 .73 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_2769 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_2769 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2769 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 ENSCJAG00000013060 1 retrocopy
retro_cjac_2769 ,


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