RetrogeneDB ID:

retro_cjac_1309

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:14:95049991..95051486(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:EFTUD2
Ensembl ID:ENSCJAG00000012349
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_cjac_1309
CCTGAGGTGCCACACTACTAAGATGTACATAGCACAAATGATGGAGTTCAGTTTCATGCCTTTGGCCCGGGTGCTGAGTG
GCACCATTCATGCTGGGCAGCCTGTGAAGGTACTCGGGGAGAACTACACCCTGGAGGATGAGGAAGACTCCCAGATATGT
ACTGTGGGCCACATTTGGATCTCTGTGGCCAGGTACCACATTGAGGTGAGCCATGTTCCTCTGGCAACTGGGTTCTGATT
GAAGGTGTTGATCAACCAGTTGTGAAGACAGCAACCATAACTGAACCCTGAGGCAATGAGGAGGCTCAGATTTTCCAGCC
CTTGAAGTTCAATGCCACATCTGTTATCAAGATTGCTGTGGAGCCAGTCAACCCCTCAGAGCTGCCCAAGATGCTTGATG
GCCTGTGCAAGGTTAACAAGAGCTATCTATCCCTCACCACCAAGGTGGATTCTGGCGAGCATGTGATTCTGGGCACCGGG
GAGCTCTACCTAGACTGTGTGATGCATGATCTACAGAAGATGTACTTGGAGATAGACATCAAGGTGGCTGACCCAGTTGT
CACATTTTGTGAGATGGTGGTGGAAACATCCTCCCTCAAGTGCTTTGCTGAAACACCTAATAAGAACAAGATCACCATGA
TTGATGAGCCTCTTGAGAAGGGCCTGGCAGAGGACATAGAGAATGAGGTGGTCCAGATTACATGGAACAGAAAGAAGCTA
GGAGAGTTCTTCCAGACCAAGTATGATTGGGATCTGCTGGCTGCCCGTTCCACCTGGGCTTTTGGCCCTGATGCCACTGG
CCCCAACATTCTGGTGGATGATACTCTACCCTCCGAGGTTGACAAGGCTCTTCTTGGCTCAGTGAAGGGCAGAATCGTTC
AAGGTTTCCAGTGGGGAACCAGGGAGGGGCCCCACTGTGATGAGTTGATTCAGAACGTCAAATTTAAGATTCTGGATGCA
GTGGTTGCCCAGGAGCCCCTGCACTGCAGCGGGGGCCAGATCATCCCCACAGCCAGGAGAGTTGTCTACTCTGCCTTCCT
CATGGCCACTCGTTGTCTGATGGAGCCTTACTACTTTGTAGAGGTCCAGGCGCCTGCAGATTGCATCTCTGTGGTTTATA
CTGTCCTAGCCAGGCGCAGAGGGCACGTGACTCGGGATGCACCCATCCCAGATTCCCCTCTGTACACCATCAAAGCTTTT
ATCCCAGCCATCGACTCTTTTGGCTTTGAAACTGATCTCCGGACTCACACCCGGGGACAGGCCTTTTCTCTGTCTGTCTT
CCACCATTGGCAGATTGTCCCTGGTGATCCTCTGGACAAGAGCATTGTCATTCGCCCTTTGGAGCCACAGCCGGCTCCTC
ACCTGGCCCGGGAATTCATGATCAAAACTTGTCGTAGGAAGGGCCTCAGTGAAGATGTGAACATAAGCAAATTCTTCGAT
GATCCTATTGTTGCTGGAACTCGCCAAACAGGATGTTGTGCTCAATTACCCCATG

ORF - retro_cjac_1309 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 90.66 %
Parental protein coverage: 51.44 %
Number of stop codons detected: 2
Number of frameshifts detected 3


Retrocopy - Parental Gene Alignment:

ParentalPLMCHTTKMYSTDDGVQFHAFG-RVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGRLWISVARYHIEV
P...H.....ST.DGVQFHAFG.RVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVG..WISVARYHIEV
RetrocopyPEVPHY*DVHSTNDGVQFHAFG>RVLSGTIHAGQPVKVLGENYTLEDEEDSQICTVGHIWISVARYHIEV
ParentalNRVP-AGNWVLIEGVDQPIVKTATITEPRGNEEAQIFRPLKFNTTSVIKIAVEPVNPSELPKMLDGLRKV
..VP..GNWVLIEGVDQP.VKTATITEP.GNEEAQIF.PLKFN.TSVIKIAVEPVNPSELPKMLDGL.KV
RetrocopySHVP<SGNWVLIEGVDQPVVKTATITEP*GNEEAQIFQPLKFNATSVIKIAVEPVNPSELPKMLDGLCKV
ParentalNKSYPSLTTKVEESGEHVILGTGELYLDCVMHDLRKMYSEIDIKVADPVVTFCETVVETSSLKCFAETPN
NKSY.SLTTKV..SGEHVILGTGELYLDCVMHDL.KMY.EIDIKVADPVVTFCE.VVETSSLKCFAETPN
RetrocopyNKSYLSLTTKVD-SGEHVILGTGELYLDCVMHDLQKMYLEIDIKVADPVVTFCEMVVETSSLKCFAETPN
ParentalKKNKITMIAEPLEKGLAEDIENEVVQITWNRKKLGEFFQTKYDWDLLAARSIWAFGPDATGPNILVDDTL
K.NKITMI.EPLEKGLAEDIENEVVQITWNRKKLGEFFQTKYDWDLLAARS.WAFGPDATGPNILVDDTL
RetrocopyK-NKITMIDEPLEKGLAEDIENEVVQITWNRKKLGEFFQTKYDWDLLAARSTWAFGPDATGPNILVDDTL
ParentalPSEVDKALLGSVKDSIVQGFQWGTREGPLCDELIRNVKFKILDAVVAQEPLHRGGGQIIPTARRVVYSAF
PSEVDKALLGSVK..IVQGFQWGTREGP.CDELI.NVKFKILDAVVAQEPLH..GGQIIPTARRVVYSAF
RetrocopyPSEVDKALLGSVKGRIVQGFQWGTREGPHCDELIQNVKFKILDAVVAQEPLHCSGGQIIPTARRVVYSAF
ParentalLMATPRLMEPYYFVEVQAPADCVSAVYTVLARRRGHVTQDAPIPGSPLYTIKAFIPAIDSFGFETDLRTH
LMAT..LMEPYYFVEVQAPADC.S.VYTVLARRRGHVT.DAPIP.SPLYTIKAFIPAIDSFGFETDLRTH
RetrocopyLMATRCLMEPYYFVEVQAPADCISVVYTVLARRRGHVTRDAPIPDSPLYTIKAFIPAIDSFGFETDLRTH
ParentalTQGQAFSLSVFHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTRRRKGLSEDVSISKFFDDP-MLL
T.GQAFSLSVFHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKT.RRKGLSEDV.ISKFFDDP..LL
RetrocopyTRGQAFSLSVFHHWQIVPGDPLDKSIVIRPLEPQPAPHLAREFMIKTCRRKGLSEDVNISKFFDDP>LLL
ParentalELAKQDVVLNYPM
ELAKQDVVLNYPM
RetrocopyELAKQDVVLNYPM

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 29 .86 RPM
SRP051959_heart 0 .00 RPM 33 .10 RPM
SRP051959_kidney 0 .02 RPM 34 .21 RPM
SRP051959_liver 0 .00 RPM 37 .41 RPM
SRP051959_lung 0 .03 RPM 35 .17 RPM
SRP051959_lymph_node 0 .00 RPM 37 .05 RPM
SRP051959_skeletal_muscle 0 .00 RPM 41 .93 RPM
SRP051959_spleen 0 .00 RPM 34 .98 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_1309 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_1309 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_1309 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 ENSCJAG00000012349 1 retrocopy
retro_cjac_1309 ,


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