RetrogeneDB ID:

retro_cfam_1023

Retrocopy
location
Organism:Dog (Canis familiaris)
Coordinates:21:43186743..43187904(+)
Located in intron of:ENSCAFG00000009933
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IDH3G
Ensembl ID:ENSCAFG00000019286
Aliases:None
Description:isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]


Retrocopy-Parental alignment summary:






>retro_cfam_1023
ATGGCACTGAAGATACTGACAGCTGCAAGTTGCTGCGTGAAGTCCATGTTGCGGCCTTGTAACCTCTGCCGTTCTTGGGA
GATTTTATGTGGCCATGAGACCTCCCCAAGGAGCTTCTCTTTTAAGTCCAGTATTCCTCCATCAGCCAAGTATGGTGGGC
GACACACTGTGACTATGATTCCTGGGGATGGCATTGGGCCTGAACTCATGCTGCATGTCAAGACTGTGTTCAGACATGCG
TGTGTGCCTGTAGACTTTGAGGAGGTGGTCGTTAACTGCACTTCTTGTGAAGAGGACATTCACAATGCCATCATGGCAGT
CCGTCGAAACCGCGTGGCTTTGAAGGGCAACCTTGAAACCGACCACAACCTGCCACCATCTCACAAATGCCGCAACAACA
TGTTTCGCACCACCCTAGATCTCTATGCCAATGTCATCCATTTTAAAAGTCTGCCAGGCGTGGAGACCCAGCACAAGGAT
GTAGACATCTTAGTTGTTCGGGAAAACACAGAGGGTGAATACAGCAACCTGGAGCACGAGAGTGTGACAGGAGTGATTGA
GAGCCTAAAGATTATTACCAAGGCCAAGTCTTTCCGCATTGCCCAATATGCCTTCCAGCTGGCCCAGGAGATGGAGCGCA
AGAAAGTGACGGTCGTGCACAAGGCTAACATCATGAAACTGGGAGATGGGCTCTTCCTGCAGTGTTGCAGGGAAGTGGCC
TCCCACTACCCTCAGCTCACCTTCGAGGGCATGATTGTGGATAACACCACCATGCAGCTAGTATCCCGGCCTCAGCAGTT
TGATGTAATGGTGATGCCCAATCTTTATGGCAACATTGTCAACAGTATCTGCACAGGATTGGTTGGGGGAGCAGGCCTTG
TGCCTGGTGCGAACTATGGCCATACACACGCAGTGTTTGAAACAGCTTCAAGGCAATCGGCCAGAAATTTAGCCAATAAG
AATATAGCCAACCCTACGGCCATGCTGCTAGCAAGCTGTATTATGCTGGACTACCTCCAGCTCCACTCCTATGCCACCTC
CATTCGCGCTGCAGTCTTGGCATCTATGGAGAACAAAAATGTCCATACTCCAGACATTGGAGGCCAGAGTACCACATTGG
ACTTCATTCATAATATAATCGACCACATCAATACTGTCCAT

ORF - retro_cfam_1023 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 75.71 %
Parental protein coverage: 98.47 %
Number of stop codons detected: 0
Number of frameshifts detected: 0


Retrocopy - Parental Gene Alignment:

ParentalMALKVAAVVRGAPKAVLRPALLCRPWEVLGAHEVPRRSVSVSTRQPPSAKYGGRHTVTMIPGDGIGPELM
MALK.........K..LRP..LCR.WE.L..HE...RS.S.....PPSAKYGGRHTVTMIPGDGIGPELM
RetrocopyMALKILTAASCCVKSMLRPCNLCRSWEILCGHETSPRSFSFKSSIPPSAKYGGRHTVTMIPGDGIGPELM
ParentalLHVKSVFRHACVPVDFEEVHVSSNADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLD
LHVK.VFRHACVPVDFEEV.V.....EEDI.NAIMA.RRNRVALKGN.ET.HNLPPSHK.RNN..RT.LD
RetrocopyLHVKTVFRHACVPVDFEEVVVNCTSCEEDIHNAIMAVRRNRVALKGNLETDHNLPPSHKCRNNMFRTTLD
ParentalLYANVIHCKSLPGVVTRHRDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQE
LYANVIH.KSLPGV.T.H.D.DIL.VRENTEGEYS.LEHESV.GV.ESLKIITKAKS.RIA.YAF.LAQE
RetrocopyLYANVIHFKSLPGVETQHKDVDILVVRENTEGEYSNLEHESVTGVIESLKIITKAKSFRIAQYAFQLAQE
ParentalSGRKKVTAVHKANIMKLGDGLFLQCCKEVAARYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
..RKKVT.VHKANIMKLGDGLFLQCC.EVA..YPQ.TFE.MIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
RetrocopyMERKKVTVVHKANIMKLGDGLFLQCCREVASHYPQLTFEGMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
ParentalNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNIANPTATLLASCMMLDHLKLHSYATSIRK
N..C.GLVGG.GLV.GANYGH..AVFETA.R......ANKNIANPTA.LLASC.MLD.L.LHSYATSIR.
RetrocopyNSICTGLVGGAGLVPGANYGHTHAVFETASRQSARNLANKNIANPTAMLLASCIMLDYLQLHSYATSIRA
ParentalAVLASMDNENMHTPDIGGQGTTSEAIQDIIRHIRIIN
AVLASM.N.N.HTPDIGGQ.TT...I..II.HI....
RetrocopyAVLASMENKNVHTPDIGGQSTTLDFIHNIIDHINTVH

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
SRP012049_cerebellum 0 .00 RPM 15 .41 RPM
SRP017611_brain 0 .00 RPM 12 .54 RPM
SRP017611_kidney 0 .00 RPM 39 .95 RPM
SRP017611_liver 0 .00 RPM 9 .14 RPM

ChIP-Seq - click to see more details

Canis familiaris was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_cfam_1023 retrocopy.

TSS - click to see more details

Canis familiaris was not studied using FANTOM5 data.

Lab - click to see more details

retro_cfam_1023 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_cfam_1023 has 7 orthologous retrocopies within eutheria group .

Species RetrogeneDB ID
Homo sapiens retro_hsap_759
Pan troglodytes retro_ptro_534
Mus musculus retro_mmus_134
Oryctolagus cuniculus retro_ocun_80
Bos taurus retro_btau_1194
Sus scrofa retro_sscr_662
Equus caballus retro_ecab_941
Parental genes homology:
Parental genes homology involve 18 parental genes, and 18 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG000000184661 retrocopy
retro_amel_1892,
Bos taurus ENSBTAG000000010591 retrocopy
retro_btau_1194,
Canis familiaris ENSCAFG00000019286 1 retrocopy
retro_cfam_1023 ,
Callithrix jacchus ENSCJAG000000111851 retrocopy
retro_cjac_1597,
Equus caballus ENSECAG000000185091 retrocopy
retro_ecab_941,
Homo sapiens ENSG000000678291 retrocopy
retro_hsap_759,
Latimeria chalumnae ENSLACG000000073651 retrocopy
retro_lcha_17,
Loxodonta africana ENSLAFG000000069041 retrocopy
retro_lafr_560,
Macropus eugenii ENSMEUG000000139341 retrocopy
retro_meug_203,
Myotis lucifugus ENSMLUG000000044571 retrocopy
retro_mluc_396,
Mustela putorius furoENSMPUG000000087811 retrocopy
retro_mputfur_644,
Mus musculus ENSMUSG000000020101 retrocopy
retro_mmus_134,
Nomascus leucogenys ENSNLEG000000135401 retrocopy
retro_nleu_394,
Otolemur garnettii ENSOGAG000000067351 retrocopy
retro_ogar_25,
Pteropus vampyrus ENSPVAG000000131631 retrocopy
retro_pvam_373,
Rattus norvegicus ENSRNOG000000372841 retrocopy
retro_rnor_209,
Sus scrofa ENSSSCG000000127831 retrocopy
retro_sscr_662,
Tursiops truncatus ENSTTRG000000117281 retrocopy
retro_ttru_848,


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