RetrogeneDB ID:

retro_cjac_178

Retrocopy
location
Organism:Marmoset (Callithrix jacchus)
Coordinates:X:123820427..123821291(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSCJAG00000023311
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:E2F6
Ensembl ID:ENSCJAG00000006910
Aliases:None
Description:E2F transcription factor 6 [Source:HGNC Symbol;Acc:3120]


Retrocopy-Parental alignment summary:






>retro_cjac_178
ATGAGTCAGCAGCAGCCTGAAGAGAACTTGCCCAACCTGCCAATGGACCTGGCGGAGGAGGCGGTTTGCCGCCAAGACGC
CACCAGTGCGGAGTGCCCGCTGCCATCAACAATAAGGGATAATTTCAGAAATGCACAACCTGAGTCTAAAATCAAAACCG
TAAATGTGAAACCTCAACGTGAGGCATCACTGGCTTGCTTAACCCGAAAATTTGTAGATATTCTCAGATTTGCTCCTGGA
GGTGTTGTTAACTTAAAGGAGGCTGCAGCAAAACTGGCAGTGCAGAAACGAAGAATATATGACATCACCAATGTCTTACT
TGGAGTCAAACTAATTGAAAAATCAGCTAAGAACCATATTCGGTGGATTGGACCAGATCTTAATCCTGCTGCAACACCCG
AAGAAAAGAAGCTACAGGAGGAACTTTGCAAATTATCAGCAACGGAAGATGCCTTAGATGGGTTAATTAATGATTGTACT
CAGCAATTGAATGAGTTAACAGATGACAAAGAAATGAAAAAACTAGCATATGTGACATATGAAGAGGTTCACAGATCTGA
ACTCTTCCAGGAACAGATCGTTTTTGTAATTAAAGCCCCAGTAGGAACCTCATTGGAAGTTTCAGGTTCCCGAGACCCTT
TCTTATTACGTCTACATAACCCCAACGAACCTATTAATGTCTGTTTGTGTGTATCGAAGGAAGATGCAGCTAACGATACA
TCTGAGGGTGCCGGGACTTCATCTGAGAGTGCTGGGACTTCATCGGAATGCGCTGGGACTTCATCTGAGAGCAGTCATCT
AGAATGCCCTGAAGAAGAAGAAAATCCTCAGCAAAGTGAAGAATTGCTTGACATGAGCAACTAA

ORF - retro_cjac_178 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 52.33 %
Parental protein coverage: 91.81 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMSQQRPARKLPSLLLDPAEETVRRRCRDPINVEGLLPSKIRINLEDNVQYVSMRKALKVKRPRFDVSLVY
MSQQ.P...LP.L..D.AEE.V.R...D....E..LPS.IR.N...N.Q..S..K...VK.P....SL..
RetrocopyMSQQQPEENLPNLPMDLAEEAVCRQ--DATSAECPLPSTIRDNFR-NAQPESKIKTVNVK-PQREASLAC
ParentalLTRKFMDLVRSAPGGILDLNKVATKLGVRKRRVYDITNVLDGIELVEKKSKNHIRWIGSDLSNFGAVPQQ
LTRKF.D..R.APGG...L...A.KL.V.KRR.YDITNVL.G..L.EK..KNHIRWIG.DL.N..A.P..
RetrocopyLTRKFVDILRFAPGGVVNLKEAAAKLAVQKRRIYDITNVLLGVKLIEKSAKNHIRWIGPDL-NPAATPEE
ParentalKKLQEELSDLSAMEDALDELIKDCAQQLFALTDDKENGRLAYVTYQDIHSIQAFHEQIVIAVKAPAETRL
KKLQEEL..LSA.EDALD.LI.DC.QQL..LTDDKE...LAYVTY...H....F.EQIV...KAP..T.L
RetrocopyKKLQEELCKLSATEDALDGLINDCTQQLNELTDDKEMKKLAYVTYEEVHRSELFQEQIVFVIKAPVGTSL
ParentalDVPAPREDSITVHIRSTKGPIDVYLCEVEQAQTGNKRAEGVGTSSSES
.V...R.D...........PI.V.LC.V......N...EG.GTSS...
RetrocopyEVSGSR-DPFLLRLHNPNEPINVCLC-VSKEDAANDTSEGAGTSSESA

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 .00 RPM 5 .57 RPM
SRP051959_heart 0 .00 RPM 9 .98 RPM
SRP051959_kidney 0 .00 RPM 7 .90 RPM
SRP051959_liver 0 .00 RPM 3 .83 RPM
SRP051959_lung 0 .00 RPM 7 .34 RPM
SRP051959_lymph_node 0 .00 RPM 7 .47 RPM
SRP051959_skeletal_muscle 0 .00 RPM 11 .44 RPM
SRP051959_spleen 0 .00 RPM 8 .40 RPM
Callithrix jacchus was not studied using ChIP-Seq data.
No EST(s) were mapped for retro_cjac_178 retrocopy.
Callithrix jacchus was not studied using FANTOM5 data.
retro_cjac_178 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cjac_178 has 1 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Pongo abelii retro_pabe_1

Parental genes homology:
Parental genes homology involve 11 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000482861 retrocopy
Callithrix jacchus ENSCJAG00000006910 1 retrocopy
retro_cjac_178 ,
Dasypus novemcinctus ENSDNOG000000002581 retrocopy
Homo sapiens ENSG000001690164 retrocopies
Macropus eugenii ENSMEUG000000079574 retrocopies
Myotis lucifugus ENSMLUG000000033841 retrocopy
Macaca mulatta ENSMMUG000000232251 retrocopy
Nomascus leucogenys ENSNLEG000000141341 retrocopy
Pongo abelii ENSPPYG000000126461 retrocopy
Pan troglodytes ENSPTRG000000116612 retrocopies
Ictidomys tridecemlineatus ENSSTOG000000033161 retrocopy



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