RetrogeneDB ID:

retro_cjac_544

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:1:71097533..71098737(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:ZNF362
Ensembl ID:ENSCJAG00000001133
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_544
AGGGTGGCCAAGCCTCGATTTAACAACCCCTACTTCTGGCCCCCTCCTCCCACCATGCCCAGCTAGCTGGATGACCTGGT
CCTGATTAACGAAATCAAGGAGCAGCTGATGGCCGAGAAGATCAGGCCACCTCACCTCAGCCTAGTCGCAGCAGCCGCTG
CTAGGGCCGCCGGCACACGCTGAGAGCAGCCAGGCCGTCATCTCGCTGCCCAAGCTGCAGCAGGTTCCGGGGCTGCATCC
GCAGGCAGTGCCGCAGCCCAACGTGGCGCTGCACGCACGGCCGGCCACCAGCACTGTCACAGGTCTGGGGCTGTCCACCC
AGACCCCGGCTGTGAGCACTTCTGAGTCGAGCACGGACACGGGCACGGGTACCAGCACCCCGTCCACACCCACCACCACC
AACCAGAGCCACCTCATCCCCTCGTCCCCCACCCTCATCTCAGGGATCACCAGCCCCCCTCTCCTGGACTCCATCAAGAC
AATCCAGGCCCATGGCCTGCTTGGCCCCTCCAAGTCCGAATGCAGCCTCAAAAAGATCAAGGCAGAGAACCCGGGGGATC
CGCCTGTCCTAGTAGTCCCCTACCCCATCCTGGCCTCGGGCAAGACTGCCAAGGAGGGCAAGATGTACAGGTGTAAGGTA
TGCCTGCTGACCTTTTTCACCAAGTCGGCTATGCAGATCCACTCCAAGTCGCACACAGAAGCCACGTACAAGTGCCTGTA
CTGCTCTTAAGTCCTTTGCCAATGCCTCCTACCTGGCCCAGCACCTGCGTATCCACCTGGGTGTCAAGCCCTACTACTGC
TCCTACTGTGATAAGTCCTTCCAGCAGCTCTCCCACCTCCAGCAGCACACCAGAATCCACACAGGCAACAGACCCTACAA
GTGCCCACATCCTGGCTGCGAGAAGGTTTTCACTCAGCTCTCCAACCTGCAGTCTCACCAGCGCTAGCACAACAAGGACA
AGCCCTACATGTGTCCCAGATGCTACGGGGCCTACTTGGACTCCGCCTCCCTGAAGATCCACCTCTCGGCCCACGCCATC
AAGCATGCCAAGGCCTACTGCTGCAGCATGTGTGGACAGGCCAAACCTCTGAGACCTACCTGATGATGAACATGTCCAAA
CACATGGTGGTGGAGCACCTGGTGAGCCATCACTCACCCCAGAGGACGAAGTCCCCCTGCATCCCGGTGCGAATCTCTCT
CATC

ORF - retro_cjac_544 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 86.55 %
Parental protein coverage: 100. %
Number of stop codons detected: 3
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalRMAEPRFNNPYFWPPPPTMPSQLDNLVLINKIKEQLMAEKIRPPHLPP-TSASSQQPLLVPPAPAESSQA
R.A.PRFNNPYFWPPPPTMPS.LD.LVLIN.IKEQLMAEKIR....PP.TSA.SQQPLL.PPA.AESSQA
RetrocopyRVAKPRFNNPYFWPPPPTMPS*LDDLVLINEIKEQLMAEKIR----PP>TSA*SQQPLLGPPAHAESSQA
ParentalVMSLPKLQQVPGLHPQAVPQPDVALHARPATSTVTGLGLSTRTPAVSTSESSAGTGTGTSTPSTPTTTSQ
V.SLPKLQQVPGLHPQAVPQP.VALHARPATSTVTGLGLST.TPAVSTSESS..TGTGTSTPSTPTTT.Q
RetrocopyVISLPKLQQVPGLHPQAVPQPNVALHARPATSTVTGLGLSTQTPAVSTSESSTDTGTGTSTPSTPTTTNQ
ParentalSRLIASSPTLISGITSPPLLDSIKTIQGHGLLGPPKSERGRKKIKAENPGGPPVLVVPYPILASGETAKE
S.LI.SSPTLISGITSPPLLDSIKTIQ.HGLLGP.KSE...KKIKAENPG.PPVLVVPYPILASG.TAKE
RetrocopySHLIPSSPTLISGITSPPLLDSIKTIQAHGLLGPSKSECSLKKIKAENPGDPPVLVVPYPILASGKTAKE
ParentalGKTYRCKVCPLTFFTKSEMQIHSKSHTEAKPHKCPHCS-KSFANASYLAQHLRIHLGVKPYHCSYCDKSF
GK.YRCKVC.LTFFTKS.MQIHSKSHTEA...KC..CS.KSFANASYLAQHLRIHLGVKPY.CSYCDKSF
RetrocopyGKMYRCKVCLLTFFTKSAMQIHSKSHTEA-TYKCLYCS>KSFANASYLAQHLRIHLGVKPYYCSYCDKSF
ParentalRQLSHLQQHTRIHTGDRPYKCPHPGCEKAFTQLSNLQSHQRQHNKDKPYKCPNCYRAYSDSASLQIHLSA
.QLSHLQQHTRIHTG.RPYKCPHPGCEK.FTQLSNLQSHQR.HNKDKPY.CP.CY.AY.DSASL.IHLSA
RetrocopyQQLSHLQQHTRIHTGNRPYKCPHPGCEKVFTQLSNLQSHQR*HNKDKPYMCPRCYGAYLDSASLKIHLSA
ParentalHAIKHAKAYCCSMCGRA-YTSETYLMKHMSKHTVVEHLVSHHSPQRTESPGIPVRISLI
HAIKHAKAYCCSMCG.A..TSETYLM..MSKH.VVEHLVSHHSPQRT.SP.IPVRISLI
RetrocopyHAIKHAKAYCCSMCGQA<QTSETYLMMNMSKHMVVEHLVSHHSPQRTKSPCIPVRISLI

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 .00 RPM 1 .55 RPM
SRP051959_heart 0 .00 RPM 8 .31 RPM
SRP051959_kidney 0 .00 RPM 6 .39 RPM
SRP051959_liver 0 .00 RPM 1 .71 RPM
SRP051959_lung 0 .00 RPM 4 .75 RPM
SRP051959_lymph_node 0 .02 RPM 3 .36 RPM
SRP051959_skeletal_muscle 0 .00 RPM 2 .25 RPM
SRP051959_spleen 0 .00 RPM 3 .97 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_544 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_544 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_544 has 0 orthologous retrocopies within eutheria group .

Parental genes homology:
Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species Parental gene accession Retrocopies number
Callithrix jacchus ENSCJAG00000001133 2 retrocopies
retro_cjac_1134, retro_cjac_544 ,


Copyright © RetrogeneDB 2014-2017