RetrogeneDB ID:

retro_cjac_4143

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:25511765..25513478(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:GUF1
Ensembl ID:ENSCJAG00000019056
Aliases:None
Description:Translation factor GUF1-A, mitochondrial [Source:UniProtKB/TrEMBL;Acc:F7IQ52]


Retrocopy-Parental alignment summary:






>retro_cjac_4143
AAGAATAATAAGCAAGTTCTCGATAAATTGTAAGTGGAACGAGAAAGAGGAATCACTGCTAAAGCACAGACAGCATCTCT
TTTTCACAATTGTGAAGGAAAGCAGTACCTTTTAAATCTCACTGATACACCGGGCCATGTTGATTTTAGTTATGAAGTAT
CCAGGTCACTTACTGCTTGCCAGGGTGTTTTACTTGTGGTTGATGCAAATGAGGGTATTCAAGCCCAAACTGTAGCAAAC
TTCTTTCTTGCCTTTGAAGCACACCTATCGGTAATTCCAGTTATAAATAAGATAGAGCTGAAGAATGCTGATCCTGAAAG
GGTTGAAAACCAAATTGAGAAAGTGTTTGATATTCCAAGTGATGAATGTATTAAGATTTCTGCTAAACTTGGAACAAACG
TTGAGAGTGTTCTTCAGGCAATTATTGAAAGAATCCCCCCTTCTAAAGTGCATCGCAAAAATCCCCTGAGAGCTTTGGTA
TTTGACTCCACCTTTGATCACTATAGAGGTGTGAAAGCCAATGTAGCATTACTTGATGGAGTGGTTTCCAAAGGAGATAA
AATTGTATCTGCACATACTCAAAAGATATACGAAGTTAATGAAGTAGGAGTTTTGAATCCTAATGAGCAGCCAACTCATA
AATTATATGCAGAACAGGTGGGCTATCTGATTGCTGGGATGAAAGATGTCACTGAAGCACAAATAGGAGATACATTACAT
TTACATAAGCAACCAGTGGAGCCCTTGACCGGGTTTAAATCAGCAAAACCAATGGTATTTGCAGGAATATATCCTGTAGA
CCGATCTGAATATAACAATCTAAAGAGTGCCATAGAGAAACTGACTTTAAATGATTCCAGTGTGACAGTTCATCAAGATA
GTAGCCTTGCTCTGGGTGCTGGCTGGAGGCTAGGTTTTCTTGGACTTTTGCACATGGAAGTATTCAACCAGCGAATAGAG
CAAGAATATAATGCTTCTGTTATTTTGACAACCCCTACTGTTCCATATAAAGCTGTACTTCCATCATCAAAACTGATAAA
GGAATATAGAGAAAAAGAAATTACAATTATAAATCCTGCACAATTCCCTGATAAATCAAAAGTAACAGAATATTTGGAGC
CAGTTGTTTTGGGTACTATTATCACACCAGATGAATACACTGGAAAAATAATGATGCTATGCCAGGCTCGAAGGGCAGTT
CAGAAGAATATGATGTTTATTGATCAAAATAGAGTTATACTTAATTATCTCTTTCCTTTGAATGAAATTGTGGTAGATTT
TTATGACGCTTTGAAATCTCTATCTTCTGGATATGCCAGTTTTGATTACGAAGATGCAGGCTACCAGACTGCAGAACTTG
TGAAAATGGATATTCTACTGAATGGAAATACCGTAGAGGAGCTGGTAACTGTTGTACACAAAGACAAAGCACACTCGATT
GGCAAAGCCATGTGTGAATGGCTCAAGGATTGTCTTCCTAGGCAACTGTTTGAGATAGCAATTCAAGCTTCTATTGGAAG
TAAAATCATTGCAAGAGAAACTGTGAAAGCCTATAGGAAAAATGTTTTGGCAAAATGTTATGGTGGTGATATTACCTGAA
AAATGAAACTTTTGAAGAGACAAGCAGAAGGGGGAAAAAAGCTGAGGAAAATTGGCAACATTGAAGTTCCAAAAGATACT
TTTATAAAAGTTCTGAAAACACAATCTTCTAAA

ORF - retro_cjac_4143 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 95.8 %
Parental protein coverage: 85.35 %
Number of stop codons detected: 2
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalKNNKQVLDKLQVERERGITVKAQTASLFHNCEGRQYLLNLIDTPGHVDFSYEVSRSLSACQGVLLVVDAN
KNNKQVLDKL.VERERGIT.KAQTASLFHNCEG.QYLLNL.DTPGHVDFSYEVSRSL.ACQGVLLVVDAN
RetrocopyKNNKQVLDKL*VERERGITAKAQTASLFHNCEGKQYLLNLTDTPGHVDFSYEVSRSLTACQGVLLVVDAN
ParentalEGIQAQTVANFFLAFEAQLSVIPVINKIDLKNADPERVENQIEKVFDIPSDECIKISAKLGTNVESVLQA
EGIQAQTVANFFLAFEA.LSVIPVINKI.LKNADPERVENQIEKVFDIPSDECIKISAKLGTNVESVLQA
RetrocopyEGIQAQTVANFFLAFEAHLSVIPVINKIELKNADPERVENQIEKVFDIPSDECIKISAKLGTNVESVLQA
ParentalIIERIPPPKVHRKNPLRALVFDSTFDHYRGVITNVALFDGVVSKGDKIVSAHTQKIYEVNEVGVLNPNER
IIERIPP.KVHRKNPLRALVFDSTFDHYRGV..NVAL.DGVVSKGDKIVSAHTQKIYEVNEVGVLNPNE.
RetrocopyIIERIPPSKVHRKNPLRALVFDSTFDHYRGVKANVALLDGVVSKGDKIVSAHTQKIYEVNEVGVLNPNEQ
ParentalPTHKLYAGQVGYLIAGMKDVTEAQIGDTLHLHKQPVEPLPGFKSAKPMVFAGIYPVDQSEYNNLKSAIEK
PTHKLYA.QVGYLIAGMKDVTEAQIGDTLHLHKQPVEPL.GFKSAKPMVFAGIYPVD.SEYNNLKSAIEK
RetrocopyPTHKLYAEQVGYLIAGMKDVTEAQIGDTLHLHKQPVEPLTGFKSAKPMVFAGIYPVDRSEYNNLKSAIEK
ParentalLTLNDSSVTVHRDSSLALGAGWRLGFLGLLHMEVFNQRLEQEYNASVILTTPTVPYKAVLSSSKLIKEYR
LTLNDSSVTVH.DSSLALGAGWRLGFLGLLHMEVFNQR.EQEYNASVILTTPTVPYKAVL.SSKLIKEYR
RetrocopyLTLNDSSVTVHQDSSLALGAGWRLGFLGLLHMEVFNQRIEQEYNASVILTTPTVPYKAVLPSSKLIKEYR
ParentalEKEITIINPAQFPDKSKVTEYLEPVVLGTIITPDEYTGKIMMLCQARRAVQKNMMFIDQNRVMLKYLFPL
EKEITIINPAQFPDKSKVTEYLEPVVLGTIITPDEYTGKIMMLCQARRAVQKNMMFIDQNRV.L.YLFPL
RetrocopyEKEITIINPAQFPDKSKVTEYLEPVVLGTIITPDEYTGKIMMLCQARRAVQKNMMFIDQNRVILNYLFPL
ParentalNEIVVDFYDSLKSLSSGYASFDYEDAGYQTAELVKMDILLNGNTVEELVTVVHKDKAHSIGKAMCERLKD
NEIVVDFYD.LKSLSSGYASFDYEDAGYQTAELVKMDILLNGNTVEELVTVVHKDKAHSIGKAMCE.LKD
RetrocopyNEIVVDFYDALKSLSSGYASFDYEDAGYQTAELVKMDILLNGNTVEELVTVVHKDKAHSIGKAMCEWLKD
ParentalCLPRQLFEIAIQASIGSKIIARETVKAYRKNVLAKCYGGDITRKMKLLKRQAEGKKKLRKIGNIEVPKDT
CLPRQLFEIAIQASIGSKIIARETVKAYRKNVLAKCYGGDIT.KMKLLKRQAEG.KKLRKIGNIEVPKDT
RetrocopyCLPRQLFEIAIQASIGSKIIARETVKAYRKNVLAKCYGGDIT*KMKLLKRQAEGGKKLRKIGNIEVPKDT
ParentalFIKVLKTQSSK
FIKVLKTQSSK
RetrocopyFIKVLKTQSSK

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 12 .60 RPM
SRP051959_heart 0 .02 RPM 15 .49 RPM
SRP051959_kidney 0 .04 RPM 19 .59 RPM
SRP051959_liver 0 .00 RPM 13 .17 RPM
SRP051959_lung 0 .00 RPM 13 .45 RPM
SRP051959_lymph_node 0 .00 RPM 19 .04 RPM
SRP051959_skeletal_muscle 0 .00 RPM 17 .40 RPM
SRP051959_spleen 0 .02 RPM 14 .52 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_4143 retrocopy.

TSS - click to see more details

Callithrix jacchus was not studied using FANTOM5 data.

Lab - click to see more details

retro_cjac_4143 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_4143 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 ENSCJAG00000019056 1 retrocopy
retro_cjac_4143 ,


Copyright © RetrogeneDB 2014-2017