RetrogeneDB ID:

retro_cjac_1871

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:2:170064642..170066181(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:DNM2
Ensembl ID:ENSCJAG00000006319
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1871
GGCAACCGCGGGATCGAAGAGCTGATCCCGCTGGTCACCAAGCTGCAGGATGACTTCAGTGCCATCAGTCAGAGCTGCCA
CGTGGCCCTGCTGCAGATCGCCGTGGTGGGCGGCCAGAGCGCAGGCAAGAGCTCGGTGCTGGAGAACTTTGTGGGCCAGG
ACTTCCTTCCCGGTGGTTCAGGTATCGTCACCGGGCAGCCTCTCATTATGCAGCTCATCTTCTCAAAAACAGAATATGCC
GAGTTTTTGCACTGCAAGTCCGAAAAGCTTACAGACTCTGATGGAGTCCAGCAGGAGATTGAAGCAGACACTAACAGGGT
CAACCAACAAAGGCATCTCCCCAGCGCCCATCAACCTTTGGGTCTACTCACCACATGTGCTGAACTTGACCCTCATCAAA
CTCCCAGGTATTGCCAAGGTGCCTGTGGGCGACCAGCCTCCAGACATCGAGTACCAGAGCAAGGACATGATCCTGCAGTT
CCTCAGCCGGAAAAGCAGCCTCATCCTGGCCGTCACGCCTGCCAACATGGACCTGGCCAATTGAGATGCTCTCAACCTGG
TCAAGAAGGTCGATCCCCAAGGCCTGCGGACCATCAGTGTCATCACCAGGCTTGACCTGATGGATGAGGGCACTGACACC
AGGGACGTCTTAAAGAACAAGATGCTCTCATTGAGATGAGGCTACATTGGTGTGGCAAACCACAGCCAGAAGGATATTGA
CTGCAAGGAGGACATCTGAGCAGCGCTGCAGCTGAGAGGAGGTTCTTCCTCTCCCACCCAGCCTACTGGCACTGACCCCA
TGGGCACACTGCACCTGCAGAAGACGTTGAATCAGTAACTGACCCACCACATCTGGGAGTCGCTGCTGGCCCTGTGTAGC
AAGCTCCAGAGCCAGCTGCTGTCCCTGGAAAATGAAGGGGAGCAGTACAAGAACTTCTGGCCTGATGACCCCACCCGCAA
AACCAAAGCCCTGCTACAGGTGGTCCAGAAGTTTGGGTTGGATTTTGAGAAGAAGATCGAGGGCTCAGGAGATCAGGTGG
ACACGCTGGAGCTCTCCGAGGGCGCCCGAATCAATCGCATCTGCCACGAGCGGTTCCCGTTTGAGCTGGTGAAGATGGAG
TTTGACGAGGACTTAAGATGGGAGATCCGCTACTCCATTAAGAACATCCACGGAGTCAGGACGTGGTTCTTCACCCCCGA
CATGGCCTTTGAGTCTATTGTGAAAAAAGAGATTGTAAAACTCAAAGAATCAAGTTTGAAGTGTGTTGATCTTGTGGTCT
CAGAGCTGGCCATGGTCGTTAAAAAGTGTGCCCAGAAGTTCAGCTTCAATCCCGGTTGTGAGAGGAGATGGAGCAAATCG
TCATCACTTGCATCTGGGAATGGGAGGGGAGAACCAAGGACCAGATTCTTCTGCTGAGCGACATCGAACAGTCCTACATT
AACACAAACCATGAGGACTTCATTGGCTTTGCCAGTGCCCAGCAGAGGAGCACACAGCTGAACAGGAAGAGGGCCATCCC
CAGTCAGGGGAAGATGCTG

ORF - retro_cjac_1871 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.27 %
Parental protein coverage: 59.54 %
Number of stop codons detected: 5
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalGNRGMEELIPLVNKLQDAFSSIGQSCHLDLPQIAVVGGQSAGKSSVLENFVGRDFLPRGSGIVTRRPLIL
GNRG.EELIPLV.KLQD.FS.I.QSCH..L.QIAVVGGQSAGKSSVLENFVG.DFLP.GSGIVT..PLI.
RetrocopyGNRGIEELIPLVTKLQDDFSAISQSCHVALLQIAVVGGQSAGKSSVLENFVGQDFLPGGSGIVTGQPLIM
ParentalQLIFSKTEYAEFLHCKSKKFTDFDEVRQEIEAETDR-VTGTNKGISPVPINLRVYSPHVLNLTLIDLPGI
QLIFSKTEYAEFLHCKS.K.TD.D.V.Q..E.E.D.....TNKGISP.PINL.VYSPHVLNLTLI.LPGI
RetrocopyQLIFSKTEYAEFLHCKSEKLTDSDGVQQ--EIEADT>TGSTNKGISPAPINLWVYSPHVLNLTLIKLPGI
ParentalTKVPVGDQPPDIEYQIKDMILQFISRESSLILAVTPANMDLANSDALKLAKEVDPQGLRTIGVITKLDLM
.KVPVGDQPPDIEYQ.KDMILQF.SR.SSLILAVTPANMDLAN.DAL.L.K.VDPQGLRTI.VIT.LDLM
RetrocopyAKVPVGDQPPDIEYQSKDMILQFLSRKSSLILAVTPANMDLAN*DALNLVKKVDPQGLRTISVITRLDLM
ParentalDEGTDARDVLENKLLPLRRGYIGVVNRSQKDIEGKKDIRAALAAERKFFLSHPAYRHMADRMGTPHLQKT
DEGTD.RDVL.NK.L.LR.GYIGV.N.SQKDI..K.DI.A..A.......S.P......D.MGT.HLQKT
RetrocopyDEGTDTRDVLKNKMLSLR*GYIGVANHSQKDIDCKEDI*A--ALQLRGGSSSPTQPTGTDPMGTLHLQKT
ParentalLNQQLTNHIRESLPALRSKLQSQLLSLEKEVEEYKNFRPDDPTRKTKALLQMVQQFGVDFEKRIEGSGDQ
LNQ.LT.HI.ESL.AL.SKLQSQLLSLE.E.E.YKNF.PDDPTRKTKALLQ.VQ.FG.DFEK.IEGSGDQ
RetrocopyLNQ*LTHHIWESLLALCSKLQSQLLSLENEGEQYKNFWPDDPTRKTKALLQVVQKFGLDFEKKIEGSGDQ
ParentalVDTLELSGGARINRIFHERFPFELVKMEFDEKDLRREISYAIKNIHGVRTGLFTPDMAFEAIVKKQIVKL
VDTLELS.GARINRI.HERFPFELVKMEFDE.DLR.EI.Y.IKNIHGVRT..FTPDMAFE.IVKK.IVKL
RetrocopyVDTLELSEGARINRICHERFPFELVKMEFDE-DLRWEIRYSIKNIHGVRTWFFTPDMAFESIVKKEIVKL
ParentalKEPSLKCVDLVVSELATVIKKCAEKLSSYP-RLREETERIVTTYIREREGRTKDQILLLIDIEQSYINTN
KE.SLKCVDLVVSELA.V.KKCA.K.S..P.RL.EE.E.IV.T.I.E.EGRTKDQILLL.DIEQSYINTN
RetrocopyKESSLKCVDLVVSELAMVVKKCAQKFSFNP<RL*EEMEQIVITCIWEWEGRTKDQILLLSDIEQSYINTN
ParentalHEDFIGFANAQQRSTQLNKKRAIPNQGEIL
HEDFIGFA.AQQRSTQLN.KRAIP.QG..L
RetrocopyHEDFIGFASAQQRSTQLNRKRAIPSQGKML

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 .04 RPM 71 .89 RPM
SRP051959_heart 0 .02 RPM 33 .91 RPM
SRP051959_kidney 4 .77 RPM 42 .77 RPM
SRP051959_liver 0 .00 RPM 28 .74 RPM
SRP051959_lung 0 .02 RPM 52 .04 RPM
SRP051959_lymph_node 0 .00 RPM 46 .48 RPM
SRP051959_skeletal_muscle 0 .00 RPM 26 .55 RPM
SRP051959_spleen 0 .02 RPM 46 .62 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_1871 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1871 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1871 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 ENSCJAG00000006319 1 retrocopy
retro_cjac_1871 ,


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