RetrogeneDB ID:

retro_cjac_511

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:26791140..26793063(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CSRP2BP
Ensembl ID:ENSCJAG00000005057
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_511
ATGGAGAGTAGCATCCACCTGAGTAGTCTGATTAGTCGGCACGGTGACGAAGCCACGAGAACACCGACCTCAGAAGGACT
GGAGGAAGGTGAAGTGGAGGGAGAGTCGCTCCTGATTGTGGAATCTGAGGATCAGGCTCAGTGGATTATCACACGACCAG
AGTGGGGATTCCCTCAACAGTGATGAAGGAGGCGTGTCGTGGATGGAGGAGCAGCTGCCCTACTTCTGTGACAAGTGCCA
AAAACGGATACCAGCCACTCAGCTGAGGGAACAGCTCAGTTACCTTAAGGGTGATAATTTTTTAGGCTTACTTGTTCAGA
TTGCTCAGCAGATGGCAAGGAGCAGCATGAAAGGCTGAAGCTGACATGGCAGCAGGTCGTCATGTTGGCGATGGACAACT
TGTCTCTAGAAGGAAGTGGACGTCAAGGTTATTTCAGGTGGAAAGAAGACATCTGCGCTTTTATTGAGAAGCATTGGACT
TTTTTACTAGGGAATAGGAAAAAGACGTCCACCTGGTGAAGCACTGTGTCAGGGTGCCTCAGCGTGGGAAGTCCCACGTA
TTTCCATTCAGGTGCTCAGGATTTGGAGAGTCGGGATGGTGCAAACTTGTTCATAACAAGCCCCAACAATGAGACCTGAA
GGAGAGAAGCTGTCTGCCTTGATTTTGAAAATACAAGTAGCCTCGAAACCAACTTTAGATCCCTTCATGACTGTCGAGGG
ACTTAGAAAAGGGGCAAGTCGGAATCCTGTAGAATCTGCCACGGAATTACAAGAGAAAAGGTCTCGAACTCAGGAAGCAA
AAGACGTTAGAAGAGCCCAAAAGGAGGCGGCTGCTTTCCTGACAGGAGCACGTCTTCTACCCCTGTAATGTTCATAAAAC
AAGGCCATAGGCCGGATGTGATTCTTGAAAAGGGAGAACTGATTGACTTTTCCTCCTTCAGCTCCTCTGACTGCACCCCG
CAGACAAGCCCATCTCCTTCTCTGGATTGCTCTGCCCCTGGGACACCTGCCTCTCATTCTGCCATGCCTAGCTTGCTTTC
AGAAGCAGATCTGATTCCAGATGTGATGCCCCCGCAAGCCTTGTTTCACGATGATGCTTAGATGGAAAGTGATGGAGTCA
TAGACCCAGGGATGGAGAACATTCCACCCCCTTCTGGGTCAGTGGCTTCTGGGCCAGTGGTTGGGGGCAGAAAGAAGGTC
AGAGGCCCTGAACAGATAAAGCAGGAGGTAGAGAGTGAGGAAGAAAAACCCGACAGGATGGATATTGACAGTGAAGACAC
AGATTCCAACCCATCTTTGCAAACAAGGGCTTGAGAAAAGAGGAAGCCTCAGCTGGAGAAGGACACAAAGGCGAAAGAGC
CCAAATATACTCCCATGAGCATCAGTGAGGAAAAGCTGTTGCCCAAGAGGCTGGAAGCTTGTCCCGGTGCGGTTGCCATG
ACTCCGGAAGCTCGGAGACTGAAGCGCAACCTGATTGTCAGACAAGCGAAAAGGGATAGGGGATTACCACTTTTTGACTT
GGATCAATTTGTTAATGCTGCTCTTCTTTTAGTTGATGGGATTTATGGAGCCAAAGACGGAGGAGTTTCCAGACTTTCAG
CTGGACAAGCCATGTACCGAACTACCTGTCAGGACTTCAGAATCCTTGACCGATACCAGACGTCCTTGGAAGGGATTTCA
ACACCAGACTACCAAGTTTTGTATCGCTTGGTAGGATCAGAAGATATGGCTGTGGACCAGACTATTGTCAGCCCTTATAC
CTCTCGGATCTTGAAACCTTATATCAGGCGTGATTGTGAAACAAAGCCACCCAAACTGCAGCTCCTATCACAGATTCGTT
CCCACCTGCACAGGAGCAACCCTCGCTGGATGCCGGAGCCCGATGCACCTCTTGATTACTGTTATATGCAGCCATATCAT
ATC

ORF - retro_cjac_511 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 85.28 %
Parental protein coverage: 82.95 %
Number of stop codons detected: 3
Number of frameshifts detected 6


Retrocopy - Parental Gene Alignment:

ParentalMESSIHLSSLISRHDDEATRTSTSEGLEEGEVEGETLLIVESEDQA-SVD-LSHDQSGDSLNSDEGDVSW
MESSIHLSSLISRH.DEATRT.TSEGLEEGEVEGE.LLIVESEDQA.SVD.LSHDQSGDSLNSDEG.VSW
RetrocopyMESSIHLSSLISRHGDEATRTPTSEGLEEGEVEGESLLIVESEDQA<SVD<LSHDQSGDSLNSDEGGVSW
ParentalIEEQLSYFCDKCQKWIPASQLREQLSYLKGDNF-FRFTCSDCSADGKEQYERLKLTWQQVVMLAMYNLSL
.EEQL.YFCDKCQK.IPA.QLREQLSYLKGDNF.FR.TCSDCSADGKEQ.ERLKLTWQQVVMLAM.NLSL
RetrocopyMEEQLPYFCDKCQKRIPATQLREQLSYLKGDNF<FRLTCSDCSADGKEQHERLKLTWQQVVMLAMDNLSL
ParentalEGSGRQGYFRWKEDICAFIEKHWTFLLGNRKKTSTWWSTVAGCLSVGSPMYFRSGAQE-FGESGWWKLVH
EGSGRQGYFRWKEDICAFIEKHWTFLLGNRKKTSTW.STV.GCLSVGSP.YF.SGAQ..FGESGW.KLVH
RetrocopyEGSGRQGYFRWKEDICAFIEKHWTFLLGNRKKTSTW*STVSGCLSVGSPTYFHSGAQD<FGESGWCKLVH
ParentalNKP-PTMKPEGEKLSASTLKIKDSFLAASKPTLDPIITVEGLRKRASRNPVESAMELKEKRSRTQEAKDI
NKP.PTM.PEGEKLSA..LKI......ASKPTLDP..TVEGLRK.ASRNPVESA.EL.EKRSRTQEAKD.
RetrocopyNKP<PTMRPEGEKLSALILKIQ----VASKPTLDPFMTVEGLRKGASRNPVESATELQEKRSRTQEAKDV
ParentalRRAQKEAAGFL-DRSTSSTPVKFISRGRRPDVILEKGEVIDFSSLSSSDRTPLTSPSPSPSLDFSAPGTP
RRAQKEAA.FL.DRSTSSTPV.FI..G.RPDVILEKGE.IDFSS.SSSD.TP.TSPSPS..LD.SAPGTP
RetrocopyRRAQKEAAAFL<DRSTSSTPVMFIKQGHRPDVILEKGELIDFSSFSSSDCTPQTSPSPS--LDCSAPGTP
ParentalASHSATPSLLSEADLIPDVMPPQALFHDDDEMEGDGVIDPGMEYIPPPSGSVASGPVVGSRKKVRGPEQI
ASHSA.PSLLSEADLIPDVMPPQALFHDD..ME.DGVIDPGME.IPP...........G.RKKVRGPEQI
RetrocopyASHSAMPSLLSEADLIPDVMPPQALFHDDA*MESDGVIDPGMENIPPXXXXXXXXXXXGGRKKVRGPEQI
ParentalKQEVESEEEKPDRMDIDSEDTDSNTSLQTRAREKRKPQLEKDTKPKEPKYTPVSIYEEKLLLKRLEACPG
KQEVESEEEKPDRMDIDSEDTDSN.SLQTRA.EKRKPQLEKDTK.KEPKYTP.SI.EEKLL.KRLEACPG
RetrocopyKQEVESEEEKPDRMDIDSEDTDSNPSLQTRA*EKRKPQLEKDTKAKEPKYTPMSISEEKLLPKRLEACPG
ParentalAVAMTPEARRLKRKLIVRQAKRDRGLPLFDLDQVVNAALLLVDGIYGAKE-GVSRLSAGQAMYRTTCQDF
AVAMTPEARRLKR.LIVRQAKRDRGLPLFDLDQ.VNAALLLVDGIYGAK..GVSRLSAGQAMYRTTCQDF
RetrocopyAVAMTPEARRLKRNLIVRQAKRDRGLPLFDLDQFVNAALLLVDGIYGAKDGGVSRLSAGQAMYRTTCQDF
ParentalRILDRYQTSLPSRKGFRHQTTKFLYRLVGSEDMAVDQSIVSPYTSRILKPYIRRRDYETKPPKLQLLSQI
RILDRYQTSL....G........LYRLVGSEDMAVDQ.IVSPYTSRILKPYI.RRD.ETKPPKLQLLSQI
RetrocopyRILDRYQTSL---EGISTPDYQVLYRLVGSEDMAVDQTIVSPYTSRILKPYI-RRDCETKPPKLQLLSQI
ParentalRSHLHRSDPRWTPEPDAPLDYCYVRPNHI
RSHLHRS.PRW.PEPDAPLDYCY..P.HI
RetrocopyRSHLHRSNPRWMPEPDAPLDYCYMQPYHI

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 0 .71 RPM 11 .47 RPM
SRP051959_heart 0 .28 RPM 10 .47 RPM
SRP051959_kidney 0 .24 RPM 14 .35 RPM
SRP051959_liver 0 .02 RPM 9 .29 RPM
SRP051959_lung 0 .20 RPM 14 .17 RPM
SRP051959_lymph_node 0 .21 RPM 13 .20 RPM
SRP051959_skeletal_muscle 0 .24 RPM 15 .42 RPM
SRP051959_spleen 0 .23 RPM 14 .01 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_511 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_511 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_511 has 0 orthologous retrocopies within eutheria group .


Parental genes homology:
Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000005057 1 retrocopy
retro_cjac_511 ,
Dasypus novemcinctus ENSDNOG000000083721 retrocopy



Copyright © RetrogeneDB 2014-2017