RetrogeneDB ID:

retro_cjac_3269

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:9:16418079..16419848(-)
Located in intron of:ENSCJAG00000020407
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:PLEKHA5
Ensembl ID:ENSCJAG00000001320
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_3269
ATGCGGATCTATTATTTCTGCACTGATACAGGAAAGGAAACGGAGTTGTGGATGAAAGCTGTGTTAGACGCTGCCCTAGT
ACAGACAGAACCTGCGAAAAGAGTGGACAAGATTACATCTGAAAATGCACCAACTAAAGAAACCAATAACCTTCCCAACC
ATAGAGTGCTGATTAAACCAGAGATCCAAAACAATCAAAAAAACAAGGAAATGAGCAAAATCAAAGAAGAAAAGGCATTA
GAAGCTGAAAAATATGGACTTCAGCAGGATGGTCAAGATAGACCCTTAACAAAATTGATAGTGTAAAGTTGAATTCTCTG
CCTTCTGAGTATGAGAGTGGGTCAGCCTGCCCTGCTTAGACTGCACACTACAGACCAGTCAACTTAAACAGTTCCGAGAA
CAAAATAGTCAGTGTTAGCCTGGCAGATCTTAGAGGTGAAAATCACCCCAGTACAGGGCCCTTATACAGAGGCTGATGGA
GTCATACAGGGAACAAATTCAGTGCAGCAATTGGAAGAGTGGATTAACATCCAGAAGGGGAGGAGTCATGAAGAAGAAAG
CAGGGGAGTAATTTCTTACCAAACATTACCAAGAAATATGCCAAGCCGCAGAGCTCAGATTATGGCCCACTACCCTGAAG
GTTACAGAACACTCCCAAGAAACAGCAAGACAAGGCCTGAAAGTATCTGCAGTGTAAACCCTTCCACTCATAACAAGACA
TCAGGACCTGGAGCAGAAGAGAAATGAGGTTCATGAGAGATGACACAATGTGGCAGCTGTACGAGTGGCAGCAGCATCAG
TTTTATAACAAACAGAGCACCCTCCCTCGACACAGTTCTTAACCCAAAACCATGGTTAATATTTCTGACCAGACAATGCA
CTCTATTCCCACATCACCTTCCCACGGGTCAATAGCTGCTTATCAGGAAGACTCCCCTCAACGAACTTACAGATCGGAAG
CATCTTCACCAATTCAGAGAGGAGATGTGACAATAGACCTCAGACACAGGGCCCATCACCCTAAGCATGTCTATGTGCCT
GACAGAGGATCAGTGCCAGCTGGACTGAACTTTATAGTCTGTTAGTCCCCAGAGCCTCCAAGGGAAAACGCTGTCACAAG
ATGAAGGCAGAGGCACATTATACAAATACAGACCCGAAGAAGTAAATATTGATGCCAAGTTAAGCCAATTATGTGAACAA
GATAAAGTGGCGCGTGCTCTGGAAGAGCAACTTCAGCAGCTCCACGAGGAGAAATACACGCTTGAGCAAGCTTTACTATA
AGCCAGCCAAGAGATAGAAATGCAGGCAGATAACCCAGCAGCCATTCAGACAGTGGTGTTACAAAGGGACGATTTACAAA
ATGGACTGCTTAGTACATCAAGAAGTTCTCCAGCCACTGCCGAATTGGAACGAGCATGGAGAGAATATGATGAGTTAGAA
CACGACGTGACTATTACCAGGAAGCAGATGCAAGAGCAGCTAGATCACCTTGGTGAAGTTCAGACGGAATCAGCAGGAAT
TCAGCGAGCACAGATTCAGAAAGAACTTTGGCGAATTCAAGATGTCATGGAAGGACTGAGTAAACACAGCAGCAAAGAGG
TACTACAGCAATAGGTATGGTAGGACCAAAGCCTTTCTCAACAGTTAAGTACAAAAATGAGGGTCCAGATTATAGACTCT
ACAAGAGCGAACCAGAGTTAACAACAGTGGCAGAAGTTGATGAATCTAATGGAGAAGAAAAATCAGAACCTGTTTTGGAG
ATAGAAACA

ORF - retro_cjac_3269 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.81 %
Parental protein coverage: 67.81 %
Number of stop codons detected: 4
Number of frameshifts detected 5


Retrocopy - Parental Gene Alignment:

ParentalMRTYYFCTDTGKEMELWMKAMLDAALVQTEPVKRVDKITSENAPTKETNNIPNHRVLIKPEIQNNQKNKE
MR.YYFCTDTGKE.ELWMKA.LDAALVQTEP.KRVDKITSENAPTKETNN.PNHRVLIKPEIQNNQKNKE
RetrocopyMRIYYFCTDTGKETELWMKAVLDAALVQTEPAKRVDKITSENAPTKETNNLPNHRVLIKPEIQNNQKNKE
ParentalMSKIEEKKALEAEKYGFQKDGQDRPLTK-INSVKLNSLPSEYESGSVCPVQTAHYRPVSLNSSENRIVNV
MSKI.E.KALEAEKYG.Q.DGQDRPLTK.I.SVKLNSLPSEYESGS.CP..TAHYRPV.LNSSEN.IV.V
RetrocopyMSKIKEEKALEAEKYGLQQDGQDRPLTK<IDSVKLNSLPSEYESGSACPA*TAHYRPVNLNSSENKIVSV
ParentalSLADLRGGNHPST-GPLYTEADRVIQRTNSMQQLEQWIKIQKGRSHEEESRGVISYQTLPRNMPSHRAQI
SLADLRG.NHPST.GP.YTEAD.VIQ.TNS.QQLE.WI.IQKGRSHEEESRGVISYQTLPRNMPS.RAQI
RetrocopySLADLRGENHPST>GP-YTEADGVIQGTNSVQQLEEWINIQKGRSHEEESRGVISYQTLPRNMPSRRAQI
ParentalMARYPEGYRTLPRNSKTRPESICSVTPSTHDKTLAPGAEEK-RRSMRDDTMWQLYEWQQRQFYNKQSTLP
MA.YPEGYRTLPRNSKTRPESICSV.PSTH.KT..PGAEEK..R.MRDDTMWQLYEWQQ.QFYNKQSTLP
RetrocopyMAHYPEGYRTLPRNSKTRPESICSVNPSTHNKTSGPGAEEK<MRFMRDDTMWQLYEWQQHQFYNKQSTLP
ParentalRHGSLSSPKTMVNISDQTMHSIPTSPSHGSIAAYQGYSPQRTYRSEVSSPIQRGDVTIDRRHRAHHPKHV
RH.S...PKTMVNISDQTMHSIPTSPSHGSIAAYQ..SPQRTYRSE.SSPIQRGDVTID.RHRAHHPKHV
RetrocopyRHSS*--PKTMVNISDQTMHSIPTSPSHGSIAAYQEDSPQRTYRSEASSPIQRGDVTIDLRHRAHHPKHV
ParentalYVPDRRSVPAGL-TLQPVSPQSLQGKTLSQDEGRATLYKYRPEEVDIDAKLSRLCEQDKVVHALEEKLQQ
YVPDR.SVPAGL.TL..VSPQSLQGKTLSQDEGR.TLYKYRPEEV.IDAKLS.LCEQDKV..ALEE.LQQ
RetrocopyYVPDRGSVPAGL>TL*SVSPQSLQGKTLSQDEGRGTLYKYRPEEVNIDAKLSQLCEQDKVARALEEQLQQ
ParentalLHKEKYMLEQALLSASQEIEMHADDPAAIQTVVLQRDDLQNGLLSTCRELSRATAELERAWREYDKLEYD
LH.EKY.LEQALL.ASQEIEM.AD.PAAIQTVVLQRDDLQNGLLST.R..S.ATAELERAWREYD.LE.D
RetrocopyLHEEKYTLEQALL*ASQEIEMQADNPAAIQTVVLQRDDLQNGLLSTSRS-SPATAELERAWREYDELEHD
ParentalVTVTRNQMQEQLDHLGEVQTESAGIQRAQIQKELWRIQDVMEGLSKH-KQQRGTTEIGMLASKPFSTVKY
VT.TR.QMQEQLDHLGEVQTESAGIQRAQIQKELWRIQDVMEGLSKH..QQRGTT.IGM...KPFSTVKY
RetrocopyVTITRKQMQEQLDHLGEVQTESAGIQRAQIQKELWRIQDVMEGLSKH<QQQRGTTAIGMVGPKPFSTVKY
ParentalKNEGPDYRLYKSEPELTTVAEVDESNGEEKSEPVSEIET
KNEGPDYRLYKSEPELTTVAEVDESNGEEKSEPV.EIET
RetrocopyKNEGPDYRLYKSEPELTTVAEVDESNGEEKSEPVLEIET

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 .02 RPM 18 .55 RPM
SRP051959_heart 0 .14 RPM 32 .36 RPM
SRP051959_kidney 0 .02 RPM 55 .04 RPM
SRP051959_liver 0 .00 RPM 18 .65 RPM
SRP051959_lung 0 .07 RPM 32 .31 RPM
SRP051959_lymph_node 0 .00 RPM 7 .79 RPM
SRP051959_skeletal_muscle 0 .00 RPM 8 .06 RPM
SRP051959_spleen 0 .02 RPM 25 .92 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_3269 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_3269 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_3269 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 ENSCJAG00000001320 1 retrocopy
retro_cjac_3269 ,


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