RetrogeneDB ID:

retro_ocun_62

Retrocopy
location
Organism:Rabbit (Oryctolagus cuniculus)
Coordinates:GL018701:6260292..6262140(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSOCUG00000021786
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:TKT
Ensembl ID:ENSOCUG00000015904
Aliases:None
Description:transketolase [Source:HGNC Symbol;Acc:11834]


Retrocopy-Parental alignment summary:






>retro_ocun_62
ATGCGGGCACGTGCAGCGCTGCGGGACGCGCCAGCCGCCTGCGGTCCGCTCGCTGAGGCACGTGCGCTGCGTTCGCACCC
ACGTCGTGCTGCAGCCGCGAGATGGTGGATTCTGTTCTTCCACACGATGAGGTACAAGCCGGCGGAGCCCGCGCACCTGG
ACAACGACCGCTTCGTCCTGTCCAAGGGCCACGCCGCGCCGCTGCTCTACGCCGCCTGGGCCGAGGCGGGCGCCGTGGGC
GAGGCGGAGCTGCTGCGCCTGCGGCAGGCGCACTGCGCCCTGGAGGGGCACCCCACGCCGCGGCTGCCCTTCGTGGACGT
GGCCACCGGCTCCCTCGGGCAGGGCCTGGGCGCCGCGTGCGGCATGGCCTACGCTGGCAAGTACCTGGACCGGGCCAGCT
ACCGCGTGTTCTGCCTGCTGGGCGACGGGGAGACGGCGGAGGGCTCGGTGTGGGAGGCGCTGGCCTTCGCCTCGCACTAC
CGCCTGGACAACCTGGTGGCCGTGCTGGACGTGAACCGCTGGGGGCAGAGCGGCGCCACGGCCCTGGGGCACCGCACCGA
CGCGTACGCGCGGCGCCTCGAGGCCTTCGGCTGGAACACCTGCCTGGTGGACGGGCACGACGTGGAAGCCTTGTGCCGGG
CCTTCCGGCGCGCGAGTCAGGTGCAGGACAAGCCCACGGCCGTCGTCGCCAAGACCTTCAAGGGCCGGGGCGTTCCGAGC
GTGGAAGACGCCGGCAGCTGGCACGGGAAAGCGCTGCCCAGGGAAGCGGCCGAGGCGGCCATCGCGCGCCTGGAGAGTCA
GATGCAGACGCAGGGCCCCTGCAGCCCCCGGCCCCCCGTGGAGGACTCCCCGCCCGTCAGCATCGCGGACATCCGGATGC
CCTCCCCGCCCGCTTACCGGGTCGGCGACCAGATGTCCACCCGGAAGGCGTGTGGCTTGGCTCTGGCCAAACTGGGCCGT
GCCAACGACAGGGTGGTCGTCCTGGACGGCGACACGCAGAACTCCACCTTTTCCGACCTCTTCAAGCAGGAGCACCCGGA
GCGCTTCGTCGAGTGCTTCGTGGCGGAGCAGAACATGGTGAGCGTGGCCTTGGGCTGCGCCGCGCGGGGCCGGGCTGTCG
CGTTCGCCTGCACCTTTGGCGCCTTCCTGACGCGAGCCTTCGATCAGATCAGGATGGCGGCCATCTCGCAAGCCAACATC
AACCTTGTGGGTTCGCACTGCGGCGTGTCCGTGGGGGAAGACGGGCCCTCCCAGATGGCGCTGGAGGACCTGGCCATGTT
CCGGAGCGTCCCCGGCTGCACCGTCTTCTACCCCAGCGACGCCGTGTCCACGGAGCACGCCGTGCACCTGGCGGCCAAGG
CCAAAGGGATGTGCTTCATCCGCACCAGCCGCCCGGACACCGCGGTCATCTACGCCGCGCAGGAGCGCTTCGAGATTGGA
CAGGCCAAGGTCGTCCGCCACAGCGCCGATGACAAGGTCACGGTGGTCGGAGCTGGGGTCACCCTGCACGAGGCCTTAGC
GGCCGCCGAGGAGCTTTCTCAAGAAGGGGTTTCCGTCCGGGTCATTGACCTCTTCACCGTCAAACCCCTGGACGCCGCCA
CCATCATCTCCAGCGCCGGAGCCACGGGAGGCCGGGTGGTCACCGTGGAGGATCACTACCGCGAGGGCGGCCTCGGAGAG
GCGGTGTGTGCGGCCGTCGCCAGGGAGCCTGCCGTCCGCGTGCACCTGCTGGCGGTGTCGGGCGTGCCTCGCAGCGGGAG
GCCCAGGGAGCTGCTGGATGCGTTTGGAATCAGCGCCGGACACATCGTGGCCGCTGTGAAGTCTGCTTTAATGCAGGAAA
ACAACTGA

ORF - retro_ocun_62 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 65.57 %
Parental protein coverage: 92.3 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalSAAEIMAVLFFHTMRYKAQDPRNPHNDRFILSKGHAAPILYAVWAEAGYLPEAELLNLRKISSDLDGHPV
.AA.....LFFHTMRYK...P....NDRF.LSKGHAAP.LYA.WAEAG...EAELL.LR.....L.GHP.
RetrocopyAAAARWWILFFHTMRYKPAEPAHLDNDRFVLSKGHAAPLLYAAWAEAGAVGEAELLRLRQAHCALEGHPT
ParentalPKQAFTDVATGSLGQGLGAACGMAYTGKYFDKASYRVYCLLGDGELSEGSVWEAMAFASFYKLDNLVAIL
P...F.DVATGSLGQGLGAACGMAY.GKY.D.ASYRV.CLLGDGE..EGSVWEA.AFAS.Y.LDNLVA.L
RetrocopyPRLPFVDVATGSLGQGLGAACGMAYAGKYLDRASYRVFCLLGDGETAEGSVWEALAFASHYRLDNLVAVL
ParentalDVNRLGQSDPAPLQHQLDVYQKRCEAFGWHTIIVDGHSVEELCKAF---GQAKHQPTAIIAKTFKGRGIT
DVNR.GQS....L.H..D.Y..R.EAFGW.T..VDGH.VE.LC.AF....Q....PTA..AKTFKGRG..
RetrocopyDVNRWGQSGATALGHRTDAYARRLEAFGWNTCLVDGHDVEALCRAFRRASQVQDKPTAVVAKTFKGRGVP
ParentalGIEDKESWHGKPLPKNMADQVIQEIYSQIQSKKKILATPPQEDAPSVDISNIRMPTPPSYKVGDKIATRK
..ED..SWHGK.LP...A...I....SQ.Q........PP.ED.P.V.I..IRMP.PP.Y.VGD...TRK
RetrocopySVEDAGSWHGKALPREAAEAAIARLESQMQTQGPCSPRPPVEDSPPVSIADIRMPSPPAYRVGDQMSTRK
ParentalAYGQALAKLGHASDRIIALDGDTKNSTFSDLFKKEHPDRFIECYIAEQNMVSVAVGCATRNRTVPFCSSF
A.G.ALAKLG.A.DR...LDGDT.NSTFSDLFK.EHP.RF.EC..AEQNMVSVA.GCA.R.R.V.F...F
RetrocopyACGLALAKLGRANDRVVVLDGDTQNSTFSDLFKQEHPERFVECFVAEQNMVSVALGCAARGRAVAFACTF
ParentalAAFFTRAFDQIRMAAISESNINVCGSHCGVSIGEDGPSQMALEDLAMFRSIPMSTVFYPSDAVATEKAVE
.AF.TRAFDQIRMAAIS..NIN..GSHCGVS.GEDGPSQMALEDLAMFRS.P..TVFYPSDAV.TE.AV.
RetrocopyGAFLTRAFDQIRMAAISQANINLVGSHCGVSVGEDGPSQMALEDLAMFRSVPGCTVFYPSDAVSTEHAVH
ParentalLAANTKGICFIRTSRPENAIIYNNSEDFQVGQGKVVLKSKDDQVTVVGAGVTLHEALAAAELLKKERISI
LAA..KG.CFIRTSRP..A.IY...E.F..GQ.KVV..S.DD.VTVVGAGVTLHEALAAAE.L..E..S.
RetrocopyLAAKAKGMCFIRTSRPDTAVIYAAQERFEIGQAKVVRHSADDKVTVVGAGVTLHEALAAAEELSQEGVSV
ParentalRVVDPFTIKPLDRKLILDSARATKGRILTVEDHYYEGGIGEAVSTAVVGEPGVTVARLAVGQVPRSGKPA
RV.D.FT.KPLD...I..SA.AT.GR..TVEDHY.EGG.GEAV..AV..EP.V.V..LAV..VPRSG.P.
RetrocopyRVIDLFTVKPLDAATIISSAGATGGRVVTVEDHYREGGLGEAVCAAVAREPAVRVHLLAVSGVPRSGRPR
ParentalELLRMFGIDKDAIAQAVR
ELL..FGI....I..AV.
RetrocopyELLDAFGISAGHIVAAVK

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
SRP017611_brain 0 .11 RPM 107 .89 RPM
SRP017611_kidney 0 .10 RPM 100 .14 RPM
SRP017611_liver 0 .00 RPM 104 .21 RPM

ChIP-Seq - click to see more details

Oryctolagus cuniculus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ocun_62 retrocopy.

TSS - click to see more details

Oryctolagus cuniculus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ocun_62 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ocun_62 has 6 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_47
Pan troglodytes retro_ptro_126
Macaca mulatta retro_mmul_74
Mus musculus retro_mmus_220
Bos taurus retro_btau_176
Equus caballus retro_ecab_6
Parental genes homology:
Parental genes homology involve 19 parental genes, and 22 retrocopies.

Species Parental gene accession Retrocopies number
Bos taurus ENSBTAG000000037581 retrocopy
retro_btau_176,
Callithrix jacchus ENSCJAG000000072531 retrocopy
retro_cjac_2128,
Cavia porcellus ENSCPOG000000000721 retrocopy
retro_cpor_45,
Dipodomys ordii ENSDORG000000013921 retrocopy
retro_dord_329,
Homo sapiens ENSG000001639311 retrocopy
retro_hsap_47,
Macropus eugenii ENSMEUG000000053123 retrocopies
retro_meug_1397, retro_meug_160, retro_meug_796,
Myotis lucifugus ENSMLUG000000009431 retrocopy
retro_mluc_67,
Macaca mulatta ENSMMUG000000144331 retrocopy
retro_mmul_74,
Mus musculus ENSMUSG000000219571 retrocopy
retro_mmus_220,
Oryctolagus cuniculus ENSOCUG00000015904 2 retrocopies
retro_ocun_319, retro_ocun_62 ,
Otolemur garnettii ENSOGAG000000169111 retrocopy
retro_ogar_5,
Ochotona princeps ENSOPRG000000098911 retrocopy
retro_opri_10,
Pan troglodytes ENSPTRG000000150241 retrocopy
retro_ptro_126,
Pteropus vampyrus ENSPVAG000000162831 retrocopy
retro_pvam_352,
Rattus norvegicus ENSRNOG000000160641 retrocopy
retro_rnor_146,
Sarcophilus harrisii ENSSHAG000000173491 retrocopy
retro_shar_827,
Sus scrofa ENSSSCG000000214081 retrocopy
retro_sscr_996,
Tupaia belangeri ENSTBEG000000121141 retrocopy
retro_tbel_3510,
Takifugu rubripes ENSTRUG000000030091 retrocopy
retro_trub_23,


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