RetrogeneDB ID:

retro_cjac_1250

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:10625251..10626602(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:HGSNAT
Ensembl ID:ENSCJAG00000003561
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1250
CCACCAGACTTAGACAAAAAAAGACACGTGTTGCTGAAGATGGATCAGGCTTTGCTACTCATTCATAATGAACTCCTTGG
GACCAACTTGACTGTCTACTGGAAATCGGAATCCTGTTATCACTGCTTGTTTCAGGTTCTGGTAAATGTTCCTCAGAGCC
CAAAAGTGGGGAAGCCTAGCACTGTAGCTGTCCCTGTCAGCACCCAGCACAGATCTATCCTACAGCTGAACAACACCTTG
GAAGAGAAAGAAGTTTGTAGGCTGGAATACGAATGTGGAGAATTTGGAAACTATTCTTTCTCGGTAAAGTACATTCATAA
TGGAGTTAGTGAAATTGCCTGTGACCGGGCTGTGAATGGGGATCCACCCGACAGTAACCTTCCCGTGAGCACTGCATTCC
TTATTGGTCTCGCTCTCATCATTGTGGTATCTTTTCTGAGGCTCTTGTGGAGTTTGGATGACTTTAATAATCGAATTTCT
AGGCCATAAGTTCTTGAGAAACTGATCGCCTCATCAATTCTGAGCTGGGATCTCCCAGCAGGACAGACCCTCTCGATAGT
GACATCCAGCCAGCAATGTGGCATCCATTTGCCCTGTGGCTCCCTCTCCATGGCACAGACACCTTCAGGGGGATTGCTGT
CATACTCATGGTCTTTGTCAATTATGGAGAAGGAAAATATTGGTACTTCAAACACACCAGTTGGAATGGGTTGACGGTGG
CTGACCTCGAGTTCCCATGGTTTGTATTTATTATGGGATCTTCCATTTTTCTATCAATCACTTCTATGCTGCAATGGGGA
TATTCAAACTTCAGAGTGCTGGGGAAGATTGCATGGAGGAGTTTCCTGTTAATCTGCATAGGAATTATCATTGTGGATCC
CAATTATTGCCTTGGTCCATTGTCTTGGGACAAGGTGCGCATTCCTGGTGTGCTGCAGCGCTGGGGGTGACTTGCTTTGT
GGTTGCTGTGTTGGAGCTCCTCTTTGTTAATCCTGTGCCTGAACATTGTGCCTCGGAGAGGAGCTGCCTTTTTCTTCGAG
ACATAATGTCCAGCTGGTCGTAGAGGCTTCACATCCTGGCGCTGGAAGGCCTGGGGCTGGGCCTGACACTCCTCCTGCCA
GTCCCTGGGTGCCCTACTGGTTATCTTGGTCCTGGGGGCATTGGAGATTTTGGCAAGTATCCAAATTGTACTGGAGGAGC
TGCGGGCTACATGGACCGCCTGCAGCTGGGAGACGATCGCCTTTACCAGCGCCCATCTTCTGCTGTGCTTTTCCACACTG
AGGTGGCCTATGATCCCGAGGACATCCTGGGCACCATCCACTCCATCGTGATGGCCTTTTTAGTAGTTCAG

ORF - retro_cjac_1250 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 83.74 %
Parental protein coverage: 87.28 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalPRDLDKKRHVELKMDQALLLIHNELLGTNLTVYWKSESCYLCLFQVLVNIPQSPKAGKPSIAATPVSTQH
P.DLDKKRHV.LKMDQALLLIHNELLGTNLTVYWKSESCY.CLFQVLVN.PQSPK.GKPS..A.PVSTQH
RetrocopyPPDLDKKRHVLLKMDQALLLIHNELLGTNLTVYWKSESCYHCLFQVLVNVPQSPKVGKPSTVAVPVSTQH
ParentalGSILQLNNTLEDKEVCRLEYKFGEFGNYSLLVKYIHNGVREIACDLAVNEDPVDSNLPVSIAFLIGLALI
.SILQLNNTLE.KEVCRLEY..GEFGNYS..VKYIHNGV.EIACD.AVN.DP.DSNLPVS.AFLIGLALI
RetrocopyRSILQLNNTLEEKEVCRLEYECGEFGNYSFSVKYIHNGVSEIACDRAVNGDPPDSNLPVSTAFLIGLALI
ParentalIVISFLRLLLSLDDFNNWISK-AISSRETDRLINSELGSPSRTDPLDGDVQPAVWRPSALPLRLRSVDTF
IV.SFLRLL.SLDDFNN.IS..AISS.ETDRLINSELGSPSRTDPLD.D.QPA.W.P.AL.L.L...DTF
RetrocopyIVVSFLRLLWSLDDFNNRISR<AISS*ETDRLINSELGSPSRTDPLDSDIQPAMWHPFALWLPLHGTDTF
ParentalRGIALILMVFVNYGGGKYWYFKHASWNGLTVADLVFPWFVFIMGTSVFLSMTSILQRGCSKFRLLGKIAW
RGIA.ILMVFVNYG.GKYWYFKH.SWNGLTVADL.FPWFVFIMG.S.FLS.TS.LQ.G.S.FR.LGKIAW
RetrocopyRGIAVILMVFVNYGEGKYWYFKHTSWNGLTVADLEFPWFVFIMGSSIFLSITSMLQWGYSNFRVLGKIAW
ParentalRSFLLICIGIIIVNPNYCLVIQPVSWDKVRIPGVLQR-LGVTYFVVAVLELLFAKPVPEHCTSERSCLSL
RSFLLICIGIIIV.PNYCL...P.SWDKVRIPGVLQR.LGVT.FVVAVLELLF..PVPEHC.SERSCL.L
RetrocopyRSFLLICIGIIIVDPNYCL--GPLSWDKVRIPGVLQR<LGVTCFVVAVLELLFVNPVPEHCASERSCLFL
ParentalRDITSSWPQWLLILALEGLWLGLTFLLPVPGCPTGYLGPGGIGDFGKYPNCTGGAAGYIDRLLLGDDHLY
RDI.SSW...L.ILALEGL.LGLT.LLPVPGCPTGYLGPGGIGDFGKYPNCTGGAAGY.DRL.LGDD.LY
RetrocopyRDIMSSWS*RLHILALEGLGLGLTLLLPVPGCPTGYLGPGGIGDFGKYPNCTGGAAGYMDRLQLGDDRLY
ParentalQHPSSAVLYHTEVAYDPEGILGTINSILMAFLGVQ
Q.PSSAVL.HTEVAYDPE.ILGTI.SI.MAFL.VQ
RetrocopyQRPSSAVLFHTEVAYDPEDILGTIHSIVMAFLVVQ

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 .11 RPM 8 .99 RPM
SRP051959_heart 0 .23 RPM 15 .58 RPM
SRP051959_kidney 0 .67 RPM 10 .21 RPM
SRP051959_liver 0 .02 RPM 7 .10 RPM
SRP051959_lung 0 .28 RPM 9 .37 RPM
SRP051959_lymph_node 3 .08 RPM 6 .14 RPM
SRP051959_skeletal_muscle 0 .20 RPM 10 .92 RPM
SRP051959_spleen 0 .40 RPM 12 .40 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_1250 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1250 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1250 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 ENSCJAG00000003561 1 retrocopy
retro_cjac_1250 ,


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