RetrogeneDB ID:

retro_ecab_941

Retrocopy
location
Organism:Horse (Equus caballus)
Coordinates:7:88922965..88924126(+)
Located in intron of:ENSECAG00000024835
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:IDH3G
Ensembl ID:ENSECAG00000018509
Aliases:None
Description:isocitrate dehydrogenase 3 (NAD+) gamma [Source:HGNC Symbol;Acc:5386]


Retrocopy-Parental alignment summary:






>retro_ecab_941
GTGGCCCTGAAGATGCTGACAGCTGCCGGTTTCTCTGGGAAGGCCATGTTCCGACCTTCCATTCTTGGCCATTCTTGGGA
GATCTTACTTGGCCGTGAAACCTCCCTGAGGAGCTTTTCTTCTAAACACAATATTCCTCCATCAGCCAAGTATGGTGGGC
GGCACACTGTGACTATGATTCCTGGGGATGGCATCGGGCCTGAACTTATGCTGCATGTCAAGACTGTGTTCAGACGTATG
TGTGTGCCTGTGGACTTTGAGGAGGTGCAGGTTAACTCCACTTCTTGCGAAGAGGACGTGCATAATGCCATCATGGCAGT
CCGTCGAAACCGTGTGGCCTTGAAGGGCAACATTGAAACTGACCACAGTCTGCCACCATCTCACAAATCCCGCAACAGCC
TGTTTCGCACCATGCTAGATCTCTATGCCAGTGTCATCCATTTTCAGAGTCTGCCGGGTGTGGAGACCCGGCACAAGAAC
GTAGACATCTTAGTTGTTCGGGAAAACACAGAGGGTGAATACAGCAACCTGGAGCATGAGAGTGTGAAAGGAGTGATAGA
GAGCCTAAAGATCATCACTAAGGCCAAGTCTTTGCGCATTGCTGAATATGCCTTCCAGCTGGCCCAGGACATGGGGCGCA
AGAAAGTGACAGCTGTGCACAAGGCCAACATCATGAAATTGGGAGATGGTCTCTTCCTCCAGTGCTGTAGGGAGGTGGCC
TCCCACTATCCTCAGCTCACCTTTGAAAGCATGATTGTCGATAACACTACCATGCAGCTGGTATCCCGCCCCCAGCAGTT
TGATGTCATGGTGATGCCCAATCTTTATGGCAACATTGTCAACAATGTCTGCACAGGGTTGGTTGGAGGAGCAGGGCTTG
TGCCTGGTGCCAACTATGGACACATATATGCAGTGTTTGAAACAGCTTCAAAGCAATCTGGCAAGAATATAGCCAATAAG
AATATGGCTAACCCTACTGCCATGCTGCTGTCGAGTTGTATTATGCTGGATTACCTCAAGCTTCACTCCTATGCCACTTC
CATACGTACTGCAGTCTTGGCATCCGTGGAGAATAAAAGTGTCCATACTCCAGACATTGGAGGCCAGAGTACCACATTGG
ATTTCATTCAAAATATCATCAACCACATCGATACTGTCAAT

ORF - retro_ecab_941 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 76.74 %
Parental protein coverage: 98.47 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMALKVATAAGGAAKAVLRPTLLCRPWEVLGAPRAPRRSFSQR-TIPPSAKYGGRHTVTMIPGDGIGPELM
.ALK..TAAG...KA..RP..L...WE.L.......RSFS....IPPSAKYGGRHTVTMIPGDGIGPELM
RetrocopyVALKMLTAAGFSGKAMFRPSILGHSWEILLGRETSLRSFSSKHNIPPSAKYGGRHTVTMIPGDGIGPELM
ParentalLHVKSVFRHACVPVDFEEVHVSSSADEEDIRNAIMAIRRNRVALKGNIETNHNLPPSHKSRNNILRTSLD
LHVK.VFR..CVPVDFEEV.V.S...EED..NAIMA.RRNRVALKGNIET.H.LPPSHKSRN...RT.LD
RetrocopyLHVKTVFRRMCVPVDFEEVQVNSTSCEEDVHNAIMAVRRNRVALKGNIETDHSLPPSHKSRNSLFRTMLD
ParentalLYANVIHCKSLPGVVTRHRDIDILIVRENTEGEYSSLEHESVAGVVESLKIITKAKSLRIAEYAFKLAQE
LYA.VIH..SLPGV.TRH...DIL.VRENTEGEYS.LEHESV.GV.ESLKIITKAKSLRIAEYAF.LAQ.
RetrocopyLYASVIHFQSLPGVETRHKNVDILVVRENTEGEYSNLEHESVKGVIESLKIITKAKSLRIAEYAFQLAQD
ParentalCGRKKVTAVHKANIMKLGDGLFLQCCKEVAAGYPQITFENMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
.GRKKVTAVHKANIMKLGDGLFLQCC.EVA..YPQ.TFE.MIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
RetrocopyMGRKKVTAVHKANIMKLGDGLFLQCCREVASHYPQLTFESMIVDNTTMQLVSRPQQFDVMVMPNLYGNIV
ParentalNNVCAGLVGGPGLVAGANYGHVYAVFETATRNTGKSIANKNVANPTATLLASCMMLDHLKLHSYATSIRK
NNVC.GLVGG.GLV.GANYGH.YAVFETA....GK.IANKN.ANPTA.LL.SC.MLD.LKLHSYATSIR.
RetrocopyNNVCTGLVGGAGLVPGANYGHIYAVFETASKQSGKNIANKNMANPTAMLLSSCIMLDYLKLHSYATSIRT
ParentalAVLASMDNENMHTPDIGGQGTTSEAIQDIIRHIRIIN
AVLAS..N...HTPDIGGQ.TT...IQ.II.HI...N
RetrocopyAVLASVENKSVHTPDIGGQSTTLDFIQNIINHIDTVN

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
SRP021940_articular_cartilage 0 .00 RPM 33 .71 RPM
SRP021940_cerebellum 0 .00 RPM 102 .05 RPM
SRP021940_embryo 0 .08 RPM 67 .26 RPM
SRP021940_placental_villous 0 .24 RPM 25 .16 RPM
SRP021940_synovial_membrane 0 .03 RPM 40 .16 RPM
SRP021940_testis 169 .77 RPM 28 .01 RPM

ChIP-Seq - click to see more details

Equus caballus was not studied using ChIP-Seq data.

EST - click to see more details

No EST(s) were mapped for retro_ecab_941 retrocopy.

TSS - click to see more details

Equus caballus was not studied using FANTOM5 data.

Lab - click to see more details

retro_ecab_941 was not experimentally validated.

Retrocopy orthology:
Retrocopy retro_ecab_941 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
Canis familiaris retro_cfam_1023
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 ENSCAFG000000192861 retrocopy
retro_cfam_1023,
Callithrix jacchus ENSCJAG000000111851 retrocopy
retro_cjac_1597,
Equus caballus ENSECAG00000018509 1 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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