RetrogeneDB ID:

retro_cjac_1709

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:19:34665536..34667048(+)
Located in intron of:ENSCJAG00000016856
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:UGP2
Ensembl ID:ENSCJAG00000006960
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1709
GAAGATCTTAGCAAAGCAATGTCTCAAGATGGCACTTCTCAGTTCCAAGAAGTCATTCGGCAAGAGCTAGATTTATCTAT
GAAGAAGGAACTAGAAAACATACTCACCACAGCATCCTCACATGAGTTTGAGCACACTAGAAAAGACCTGGATGGATTTT
GGAAGCTATTTCATTGATTTTTGCAAGAAAAGGGGCCTTCTGTGGATTGGGGAAAAATTCAGAGACCTCCAGAAGATTCT
ATTCAACCCTATGAAAAGATAAAGGCCAGGGGCTTGCCTGATATATATCTTCTGTGTTGAACAAACTAGTGGTGGTGAAA
CTCAGTGGTGGTTTGGGAACCAGCATGGGCTGCAAAGGCCCTAAAAGTCTTATTGGTGTGAGGAATGAGAATACCTTTCT
GGATCTGACTGTTCAGCAAATCGAACATTTGAATAAAACCTACAATACAGATGTTCTCCTTGTTTTAATGAACTATTTTA
ACACAGATGAAGATACCAAAAAAATACTACAGAAGTACAGTCATTGTTGTGTGAAAATCTACACTTTTAATAAAAGCAGG
TACCCGAGGATTAATAAGGAATCTTTACTTCCTGTAGCAAAGAATGTGTCTTACTCAGGGGAAAATACAGAAGCTTGGTA
CCCTCCAGGTCATGGTGATATTTACGCCAGTTTCTACAACTCTGGTTAGCTTGATACCTTTATAGGAGAAGGCAAAGAGT
ATATTTTTGTGTCTAACTTAGATAATCTCGGTGCCACAGTGGATCTGTATATTCTTAATCATCTAATGAACCCACCCAAT
GGAAAATGCTGTGAATTTGTCATGGAAGTCACAAATAAAACACGTGCAGATGTAAAGGGTGGGACACTCACTCAATATGA
AGGCAAACTGAGACTGGTGGAAATTGCTCAAGTGCCAAAAGCACATGTTGATGAGTTCAAGTCTGTGTCAAAGTTCAAAA
TATTTAACATAAACAACCTATGGATTTCTCCTGCAGCAGTTAAAAGACTGCAGGAGCAGAATGCCATTGACGTGGAAATC
ATTGTGAATGCAAAGACTTTGGATGGAGGCCTGAATGTCATTCAGTTAGAAACTGCAGTAGGGGCTGCCATCGAACGTTT
TGAGAATTCTCTAGGTATTAATGTGCCAAGGAGCCATTTTCTGCCTGTCAAAACCACATCAGATCTCTTGCTGGTGATGT
CAAACCTCTATAGCCTTAATGCAGGATCTCTGACAATGAGTGATAAGCGGGAATTTCCTACAATGCCCTTGGTTAAATTA
GGCAGTTCTTTTACAAAGTTTCAAGATTATCTAAGAAGATTTGAAAGTATACCAGATATTCTTGAATTGGATCACCTCAC
AGTTTCAGGAGATGTGACATTTGGAAAGAATGTTTCATTAAAGGGAGGGAACTGTTATCATTATTGCAAATCATGGTGGC
AGAATTGACATCCCACCTGGAGCAGTATTCGAGAACCAGATTGTATCTGGGAACCTTCACATCTTGGACCAC

ORF - retro_cjac_1709 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 92.09 %
Parental protein coverage: 99.02 %
Number of stop codons detected: 2
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalQDLSKAMSQDGASQFQEVIRQELELSVKKELEKILTTASSHEFEHTKKDLDGFRKLFHRFLQEKGPSVDW
.DLSKAMSQDG.SQFQEVIRQEL.LS.KKELE.ILTTASSHEFEHT.KDLDGF.KLFH.FLQEKGPSVDW
RetrocopyEDLSKAMSQDGTSQFQEVIRQELDLSMKKELENILTTASSHEFEHTRKDLDGFWKLFH*FLQEKGPSVDW
ParentalGKIQRPPEDSIQPYEKIKARGLPD-NISSVLNKLVVVKLNGGLGTSMGCKGPKSLIGVRNENTFLDLTVQ
GKIQRPPEDSIQPYEKIKARGLPD..ISSVLNKLVVVKL.GGLGTSMGCKGPKSLIGVRNENTFLDLTVQ
RetrocopyGKIQRPPEDSIQPYEKIKARGLPD<YISSVLNKLVVVKLSGGLGTSMGCKGPKSLIGVRNENTFLDLTVQ
ParentalQIEHLNKTYNTDVPLVLMNSFNTDEDTKKILQKYNHCRVKIYTFNQSRYPRINKESLLPVAKDVSYSGEN
QIEHLNKTYNTDV.LVLMN.FNTDEDTKKILQKY.HC.VKIYTFN.SRYPRINKESLLPVAK.VSYSGEN
RetrocopyQIEHLNKTYNTDVLLVLMNYFNTDEDTKKILQKYSHCCVKIYTFNKSRYPRINKESLLPVAKNVSYSGEN
ParentalTEAWYPPGHGDIYASFYNSGLLDTFIGEGKEYIFVSNIDNLGATVDLYILNHLMNPPNGKRCEFVMEVTN
TEAWYPPGHGDIYASFYNSG.LDTFIGEGKEYIFVSN.DNLGATVDLYILNHLMNPPNGK.CEFVMEVTN
RetrocopyTEAWYPPGHGDIYASFYNSG*LDTFIGEGKEYIFVSNLDNLGATVDLYILNHLMNPPNGKCCEFVMEVTN
ParentalKTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFNTNNLWISLGAVKRLQEQNAIDMEIIV
KTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFN.NNLWIS..AVKRLQEQNAID.EIIV
RetrocopyKTRADVKGGTLTQYEGKLRLVEIAQVPKAHVDEFKSVSKFKIFNINNLWISPAAVKRLQEQNAIDVEIIV
ParentalNAKTLDGGLNVIQLETAVGAAIKSFENSLGINVPRSRFLPVKTTSDLLLVMSNLYSLNAGSLTMSEKREF
NAKTLDGGLNVIQLETAVGAAI..FENSLGINVPRS.FLPVKTTSDLLLVMSNLYSLNAGSLTMS.KREF
RetrocopyNAKTLDGGLNVIQLETAVGAAIERFENSLGINVPRSHFLPVKTTSDLLLVMSNLYSLNAGSLTMSDKREF
ParentalPTVPLVKLGSSFTKVQDYLRRFESIPDMLELDHLTVSGDVTFGKNVSLKG-TVIII-ANHGDRIDIPPGA
PT.PLVKLGSSFTK.QDYLRRFESIPD.LELDHLTVSGDVTFGKNVSLKG....II.ANHG.RIDIPPGA
RetrocopyPTMPLVKLGSSFTKFQDYLRRFESIPDILELDHLTVSGDVTFGKNVSLKG>GTVIIIANHGGRIDIPPGA
ParentalVLENKIVSGNLRILDH
V.EN.IVSGNL.ILDH
RetrocopyVFENQIVSGNLHILDH

Legend:
*Stop codon
>Forward frameshift by one nucleotide
<Reverse frameshift by one nucleotide






(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 .51 RPM 57 .09 RPM
SRP051959_heart 1 .26 RPM 85 .37 RPM
SRP051959_kidney 1 .35 RPM 36 .54 RPM
SRP051959_liver 1 .49 RPM 394 .68 RPM
SRP051959_lung 1 .97 RPM 36 .49 RPM
SRP051959_lymph_node 2 .63 RPM 32 .01 RPM
SRP051959_skeletal_muscle 1 .48 RPM 347 .75 RPM
SRP051959_spleen 2 .75 RPM 36 .81 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_1709 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_1709 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1709 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000006960 1 retrocopy
retro_cjac_1709 ,
Cavia porcellus ENSCPOG000000084591 retrocopy
Microcebus murinus ENSMICG000000065091 retrocopy
Oryctolagus cuniculus ENSOCUG000000021371 retrocopy
Tursiops truncatus ENSTTRG000000006941 retrocopy



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