RetrogeneDB ID:

retro_cjac_3922

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:GL286253.1:65993..67710(+)
Located in intron of:ENSCJAG00000012992
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ADAD1
Ensembl ID:ENSCJAG00000002796
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3922
AGCAACAACAATTGGTTTCAGAGTTTGCAGGCCCCCAGTTTTGCACAGATGCTGAAAAAGAACCTCCAGTTCAACCAGCC
ACACAGACGGTAACTACACCCACAGGATGTTTCTCAGAAAGTTATAGCCTGTCCAAGATAGCATCCAAAGTTACACAAGT
GACAGGTAATTTCCAGAACTGTTGCTTTCCAAGAGTCTTTCATCTATTTCAAATCCTGTCCTTCCTCCAAAAAAAAATAC
CTAAGGAATTTATAATGAAATACAAAGGTGGAGAGATAAATCCTGTGTCAGCCTTGCACCAGTTTGTACAAATGCAGTGA
GTTCAGCTTGACCTTAAGGAAACTGTGACAACAGATAATGTTATGGGACCGTATTTTGCCTTTTGTGCTGTGGTAGATGG
TATTCAGTACTAGACTGGACTGGGACAAAATAAAAAGGAGTCTAGATCCAATGCAGCAAAATTAGCTCTTGAGCTTCTGC
AATTGGATGAACCTGAACCACAAATTTTAGAAACATCAGATCCTCCTCCTTTCCCTGCAGAACCTACTGTTTTACCTGAA
CAGGCATATGTTTCAAAAGCACATTATGAAGGGAGATATATTCAGTATGCAAAGATTTCACAGATCGTTAAGGAAACATT
TAATCAACTAATTTCAAATCATTCAGAATGCCTGAAATGCAGCAATTCATTGGCTGCTTTTATAATTGAAAGAGCTGGAC
AGCATGAGGTTGTAGCTATAGGCACAGGTTAATACAACTACAGCCAGGGCATTAAACCAAATGGAAGAGTATTGCATGAT
ACTCATGCTGTCATTACAGCAAGAAGGTCTCTTCTTAGGTACTTTTACAGACCACTTCTACTCTTCTACAGCAAAAATCC
TGCTATGATGGAAAAATCAATATTCTGTACAGAACCAACTTCTAATCTACTCACTCTTAAACAGAATATCAACATTTGTC
TTTACATGAACCAGTTGCCTAAAGGATCAGCCCGGATTAAGTCACACTTACGTCTTAATCCACATTCTATATCTGCATTC
GAAGCCAATGAAGAACTGTGTCTCCATGTGGCTGTTGAAGGCAAAATTTATTGACTGTTTACTGTCCTAAAGATGGTGTT
AATAGAATAAGCAGTATGTCCTCAAGTGACAAATTGACAAGATGGGAAGTGTTTGGTATACAGGAAGCATTGCTGAGTCA
TTTTATACAGCTAGTTTACATCAGCAGTATACTGGTTGGTGATGGGAATTGCAATGATACCAGAGGCTTCAAAATCGCTA
TAAAGCAATGTGTTGATGATGCACTCACTTCAAAACTTCCTGTGTTTTACTTAGTCAACAGACCTCATATTAGTTTAGTG
CCCTCGGCATATCCACTTCAAATGAACTTGGAATATAAATTTCTGAGTCTGAATTGGGCACAAGGAGATGTTTCTTTGGA
GATTGTGGATGGCCTGAGTGGGAAGATCACTGAAAGTTCCCCATTTAAAAGTGGTATGTCAATGGCAAGTCAGCTTTGCA
AGGCTGCAATGTTAAGTCAATTTAACGTCCTTGCCAAAGAAGCTAAAAAAGAATTACCTGAAGCTGGTACATATCATGCA
GCTAAGTGTATGTCTTCCTCCTATCAATAAGCTAAATCTAAGCTGAAATCCTACTTACAACAACATGGCTATGGATCCTG
GATTGTGAAATCTCCCTGCATAGAGCAATTTAATATG

ORF - retro_cjac_3922 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.22 %
Parental protein coverage: 99.83 %
Number of stop codons detected: 4
Number of frameshifts detected 4


Retrocopy - Parental Gene Alignment:

ParentalASNNWFQSSQVPSFAQMLKKNL-PVQPATQMVTTPTGCFSESYSLSKMASKVTPVTGNF-PEPMLSKSLS
..NNWFQS.Q.PSFAQMLKKNL.PVQPATQ.VTTPTGCFSESYSLSK.ASKVT.VTGNF.PE..LSKSLS
RetrocopySNNNWFQSLQAPSFAQMLKKNL<PVQPATQTVTTPTGCFSESYSLSKIASKVTQVTGNF<PELLLSKSLS
ParentalSISNPVLPPKK-IPKEFITKYKRGEINPVSALHQFAQMQRVQLDLKETVTTGNVMGPYFAFCAVVDGIQY
SISNPVLPPKK.IPKEFI.KYK.GEINPVSALHQF.QMQ.VQLDLKETVTT.NVMGPYFAFCAVVDGIQY
RetrocopySISNPVLPPKK>IPKEFIMKYKGGEINPVSALHQFVQMQ*VQLDLKETVTTDNVMGPYFAFCAVVDGIQY
ParentalKTGLGQNKKESRSNAAKLALDELLQLDEPEPQVLETSALKEFPEHPVELSKK-YIGMVFFLLKKVQVLEI
.TGLGQNKKESRSNAAKLAL.ELLQLDEPEPQ.LETS....FP..P..L....Y...........Q...I
Retrocopy*TGLGQNKKESRSNAAKLAL-ELLQLDEPEPQILETSDPPPFPAEPTVLPEQAYVSKAHYEGRYIQYAKI
ParentalSNFFKKRSNTSRCRRNSHILYSTKLEMLLFLLAGQLEVVAIGTGEYNYSQSIKPNGRVLHDTHAVVTARR
S...K...N............S..L.......AGQ.EVVAIGTG.YNYSQ.IKPNGRVLHDTHAV.TARR
RetrocopySQIVKETFNQLISNHSECLKCSNSLAAFIIERAGQHEVVAIGTG*YNYSQGIKPNGRVLHDTHAVITARR
ParentalSLLRYFYRQLLLFYSKNPAMMEKSIFCTEPTSNLLTLKQNINICLYMNQLPKGSAQIKSQLRLNPHSISA
SLLRYFYR.LLLFYSKNPAMMEKSIFCTEPTSNLLTLKQNINICLYMNQLPKGSA.IKS.LRLNPHSISA
RetrocopySLLRYFYRPLLLFYSKNPAMMEKSIFCTEPTSNLLTLKQNINICLYMNQLPKGSARIKSHLRLNPHSISA
ParentalFEANEELCLHVAVEGKIY-LTVYCPKDGVNRISSMSSSDKLTRWEVLGVQGALLSHFIQPVYISSILVGD
FEANEELCLHVAVEGKIY.LTVYCPKDGVNRISSMSSSDKLTRWEV.G.Q.ALLSHFIQ.VYISSILVGD
RetrocopyFEANEELCLHVAVEGKIY<LTVYCPKDGVNRISSMSSSDKLTRWEVFGIQEALLSHFIQLVYISSILVGD
ParentalGNCSDTRGLEIAIKQRVDDALTSKLPMFYLVNRPHISLVPSAYPLQMNLGYKFLSLNWAQGDVSLEIVDG
GNC.DTRG..IAIKQ.VDDALTSKLP.FYLVNRPHISLVPSAYPLQMNL.YKFLSLNWAQGDVSLEIVDG
RetrocopyGNCNDTRGFKIAIKQCVDDALTSKLPVFYLVNRPHISLVPSAYPLQMNLEYKFLSLNWAQGDVSLEIVDG
ParentalLNGKITESSPFKSGMSMASRLCKAAMLSRFNLLAKEAKKELLEAGTYHAAKCMSSSYQEAKSKLKSYLQQ
L.GKITESSPFKSGMSMAS.LCKAAMLS.FN.LAKEAKKEL.EAGTYHAAKCMSSSYQ.AKSKLKSYLQQ
RetrocopyLSGKITESSPFKSGMSMASQLCKAAMLSQFNVLAKEAKKELPEAGTYHAAKCMSSSYQ*AKSKLKSYLQQ
ParentalHGYGSWIVKSPCIEQFNM
HGYGSWIVKSPCIEQFNM
RetrocopyHGYGSWIVKSPCIEQFNM

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 .00 RPM 0 .00 RPM
SRP051959_heart 0 .26 RPM 0 .00 RPM
SRP051959_kidney 0 .00 RPM 0 .00 RPM
SRP051959_liver 0 .00 RPM 0 .00 RPM
SRP051959_lung 0 .00 RPM 0 .23 RPM
SRP051959_lymph_node 0 .00 RPM 0 .00 RPM
SRP051959_skeletal_muscle 0 .00 RPM 0 .02 RPM
SRP051959_spleen 0 .00 RPM 0 .00 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_3922 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3922 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3922 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 ENSCJAG00000002796 1 retrocopy
retro_cjac_3922 ,


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