RetrogeneDB ID:

retro_cjac_2016

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:20:29368615..29370012(-)
Located in intron of:ENSCJAG00000014275
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CAPRIN1
Ensembl ID:ENSCJAG00000010542
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_2016
AATGCCGTTTCTAAGTACCAGGAAGTCACAAATAATTTGGAGTTTGCAAAAGAATTACAGAGGAGTTTCATGGCACTAAG
TCAAGATATTCAGAAAACAATAAAGAAGACAGCACCTCGGGAGCAGCTTATGAGAGAAGAAGCTGAACAGAAACGTTTAA
AAACTGTACTTGAGTTACAGTATGTTTTGGACGAATTGGGAAACGACGAAGTGCGAACTGACCTGAAACAAGGTTCGAAT
GGAGTGCCTATATTGTCCGAAGAGGAATTGTCATTGTTGGATGAATTCTGTAGGTTAGTAGACCCTGAACGGGACGTGAG
CTTGAGGTTGAATGAACAGTGTGAACATGCCTCCATTCACCTGTGGGTCCTGCTGGAAGGGAAGGAAAAATCTGTATGTG
GAATCACCTGTAAAGTTCTAAAAGACATTGTCGAGTGTGTTTTTCAATGAAACTACTTTGACAGCACCCACAACCACCAG
AATGGGTTGTGTGAGGAAGAAGAGGCAGCCTCAGCACCTACAATTGAAGACCAGGTAGCTGAAGCTGAACCTGAGCCAGT
GGAAGACTACACTGAGCAAAATGAAGTTGAGTCAGCAGAGTATGTAAATAGACAGTTCATGGCAGAAACACAGTTCACCA
GTGGCGAAAAGGAGCAGGTAGATGAGTGGGCAGTTGAAACAGTTGAGGTGGTAGATTCATTCCAGCAGCAGCCTCAGGCT
TCATCCCCTTCAGTACCACAACCCCACTCTTTGACTCCTGTGGCTCAAGCAGATCCCCTTCTGAGAAGACAGCGAGTACA
GGACCTTATGGCACAAATGCAGGGTCCCTATAATTTCGTACAGGATTCAGTGCTGGATTTTGAAAACCAGACACTTGATC
CTGCCATTGTATCTGCACAGCCTGTGAGTCCAGCACAAAACATGGGCATGCCCCAGCTGGTTTGCCCTCCACTTCATTCT
GAATCTAGACTTGCTCAGCCTATCAAGTTCCTGTACAACCAGAAGCTACACGGGTTCCTCTGGTGTCATCCACAAGTGAG
GGGTATACGGCATCTCAACGCCTGTACCAGCCTTCTCCTGCTACAGAGCCACGACCACAGAAGGAACCAATTGATCAGAT
TCAGGCAACAATCTCTTTAAATACAGACCGGATTACAGCATTATGATCCCTTCCTGATGCTTCTCAGCCCCAAGTACTTC
AGGCTGGGACAAGCAAACCTTTATGTAGTGGTGGAATCAATGTAAATGCAGCTCCATTCTAATCCATGCAAACGGTGTTC
AGTATGAATGCCCCAGTTCCTCCAGTTAATGAACCAGAAACTTTAATACAGCAAACTCAGTACCAGGCCAGTTATAACCA
GAGCTTTTCTAGTCAGTCTCACCAAGTAGAACAAACA

ORF - retro_cjac_2016 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 88.7 %
Parental protein coverage: 71.89 %
Number of stop codons detected: 3
Number of frameshifts detected 1


Retrocopy - Parental Gene Alignment:

ParentalDAVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTARREQLMREEAEQKRLKTVLELQYVLDKLGDDE
.AVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTA.REQLMREEAEQKRLKTVLELQYVLD.LG.DE
RetrocopyNAVSKYQEVTNNLEFAKELQRSFMALSQDIQKTIKKTAPREQLMREEAEQKRLKTVLELQYVLDELGNDE
ParentalVRTDLKQGLNGVPILSEEELSLLDEFYKLVDPERDMSLSKRLNEQYEHASIHLWDLLEGKEKSVCGTTYK
VRTDLKQG.NGVPILSEEELSLLDEF..LVDPERD.SL..RLNEQ.EHASIHLW.LLEGKEKSVCG.T.K
RetrocopyVRTDLKQGSNGVPILSEEELSLLDEFCRLVDPERDVSL--RLNEQCEHASIHLWVLLEGKEKSVCGITCK
ParentalVLKEIVERVFQSNYFDSTHNHQNGLCEEEEAASAPTVEDQVAEAEPEPAEEYTEQNEVESTEYVNRQFMA
VLK.IVE.VFQ.NYFDSTHNHQNGLCEEEEAASAPT.EDQVAEAEPEP.E.YTEQNEVES.EYVNRQFMA
RetrocopyVLKDIVECVFQ*NYFDSTHNHQNGLCEEEEAASAPTIEDQVAEAEPEPVEDYTEQNEVESAEYVNRQFMA
ParentalETQFTSGEKEQVDEWTVETVEVVNSLQQQPQAASPSVPEPHSLTPVAQADPLVRRQRVQDLMAQMQGPYN
ETQFTSGEKEQVDEW.VETVEVV.S.QQQPQA.SPSVP.PHSLTPVAQADPL.RRQRVQDLMAQMQGPYN
RetrocopyETQFTSGEKEQVDEWAVETVEVVDSFQQQPQASSPSVPQPHSLTPVAQADPLLRRQRVQDLMAQMQGPYN
ParentalFIQDSMLDFENQTLDPAIVSAQPMNPAQNMDMPQLVCPPVHSESRLAQP-NQVPVQPEATQVPLVSSTSE
F.QDS.LDFENQTLDPAIVSAQP..PAQNM.MPQLVCPP.HSESRLAQP..QVPVQPEAT.VPLVSSTSE
RetrocopyFVQDSVLDFENQTLDPAIVSAQPVSPAQNMGMPQLVCPPLHSESRLAQP<YQVPVQPEATRVPLVSSTSE
ParentalGYTGSQPLYQPSHATEQRPQKEPIDQIQATISLNTDQTTASSSLPAASQPQVFQAGTSKPLHSSGINVNA
GYT.SQ.LYQPS.ATE.RPQKEPIDQIQATISLNTD..TA..SLP.ASQPQV.QAGTSKPL.S.GINVNA
RetrocopyGYTASQRLYQPSPATEPRPQKEPIDQIQATISLNTDRITAL*SLPDASQPQVLQAGTSKPLCSGGINVNA
ParentalAPFQSMQTVFNMNAPVPPVNEPETLKQQNQYQASYNQSFSSQPHQVEQT
APF.SMQTVF.MNAPVPPVNEPETL.QQ.QYQASYNQSFSSQ.HQVEQT
RetrocopyAPF*SMQTVFSMNAPVPPVNEPETLIQQTQYQASYNQSFSSQSHQVEQT

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 3 .37 RPM 113 .20 RPM
SRP051959_heart 2 .21 RPM 74 .34 RPM
SRP051959_kidney 3 .28 RPM 114 .37 RPM
SRP051959_liver 2 .12 RPM 78 .35 RPM
SRP051959_lung 3 .14 RPM 110 .08 RPM
SRP051959_lymph_node 3 .38 RPM 107 .26 RPM
SRP051959_skeletal_muscle 0 .59 RPM 43 .68 RPM
SRP051959_spleen 2 .92 RPM 120 .74 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_2016 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_2016 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_2016 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 1 parental gene, and 4 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000010542 4 retrocopies



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