RetrogeneDB ID:

retro_lcha_17

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH128302.1:313608..314760(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLACG00000008004
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:IDH3G
Ensembl ID:ENSLACG00000007365
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_17
TCTGCCAAGCTTCTCTTTGGTAGGCGCCCCTTTGGCAACCTTATTTTCTCAGGCACTATTAAGGTGGCCCAGGAACAACC
TTTGACAGAGATCAAGCGGGAATTTTGTGCCAAACCTCAGATTACTCAGTATGGGGGCAGACGCTTGGTCACTATGATCC
CTGGGGATGGCATAGGCCCAGAGATCATGAGGTACATTCAGGAAGTGTTTAGCCATGCAGGTGTGCCTGTAGACTTTGAG
GTAATAAATGTTAACTCTTCGGGACCTAATGAAGAAATTAATAATGCCATTTCCTCCCTCAGGAAGAATGGCACAGGGAT
AAAAGGCAGCATTGAGACCAACCATGACTTGCCTCCCAACTACAAGTCAAAGAATGTTTTGCTGAGAACAAATCTTGACT
TGTTTGCTAATCTGGTCCACCATCGTAATTTCCCTGGACTTCCCAGCAAACTTGGTGCTATTGATATTGTGGTTATCAGG
GAAAACACAGAGGGAGAATATTCAAATTTGGAGCATGAGAATGTGCCAGGAGTTGTAGAGTGTTTAAAGATCATTACAAG
GCATAATTCACTGAGAATTGCCCGGTACGCTTTTGATTATGCCCGCAAGCATGGTCGGAAAAAGGTGACTGCAGTGCACA
AGGCAAATATCATGAAGCTTGGAGATGGCCTCTTTCTTGATTGCTGCAAAAAGGTTGCATCGGACTACCCAGATATTGCT
TATGAGCAAATGATTGTTGACAACACCGCTATGCAGTTGGTTGATGATCCCGCCCAGTTTGATGTGATGGTGATGCCAAA
CCTGTATGGGAACATTGTTAACAATATCTGCACTGGATTAGTCGGAGGGCCTGGACTTGTTCCGGGGGCCAACTATGGAC
ATAAGTATTCTCTCTTTGAGGCTGGCGCTCGGCATTCGGGAAAAAGCATTGCAAACAGAAATCTGGCTAACCCTACTGCC
ATGTTACTGGCAAGTTGCCTCATGTTAGATCATCTTGAATTAAAAGAGTATGCTTGGTTGATTAGAAATGCTGCCATAAA
GAGCATTGGGGATCTGAAGATCCAGACAGTTGATCTTGGAGGCTCTGCATCTACCACGGATGTCATTCACTCTGTATTGA
ATCAGATAGATGTAGCAATAGGTAGGAAACCC

ORF - retro_lcha_17 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 64.31 %
Parental protein coverage: 84.75 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalPLPAKYGGRHTVTMIPGDGIGPELMLHVKEVFRSACVPVDFEEVNVNSSKPSEDDIHNAITAIRRNRVAL
P....YGGR..VTMIPGDGIGPE.M....EVF..A.VPVDFE..NVNSS.P.E..I.NAI...R.N....
RetrocopyPQITQYGGRRLVTMIPGDGIGPEIMRYIQEVFSHAGVPVDFEVINVNSSGPNEE-INNAISSLRKNGTGI
ParentalKGNIETNHTLPASHKSRNSLLRTTLDLYANVIHCQSLPGVQTRHKDIDILIVRENTEGEYSNLEHENVPG
KG.IETNH.LP...KS.N.LLRT.LDL.AN..H....PG.......IDI...RENTEGEYSNLEHENVPG
RetrocopyKGSIETNHDLPPNYKSKNVLLRTNLDLFANLVHHRNFPGLPSKLGAIDIVVIRENTEGEYSNLEHENVPG
ParentalVVESLKIITKTNSLRIAEYAFKLAREKDRKKVTAVHKANIMKLGDGLFLQCCREVAAGYPDISFENMIVD
VVE.LKIIT..NSLRIA.YAF..AR...RKKVTAVHKANIMKLGDGLFL.CC..VA..YPDI..E.MIVD
RetrocopyVVECLKIITRHNSLRIARYAFDYARKHGRKKVTAVHKANIMKLGDGLFLDCCKKVASDYPDIAYEQMIVD
ParentalNTTMQLVSRPQQFDVMVMPNLYGNVVNNVCAGLVGGPGLVPGANYGTAYAIFETATRNTGKSIANKNIAN
NT.MQLV..P.QFDVMVMPNLYGN.VNN.C.GLVGGPGLVPGANYG..Y..FE...R..GKSIAN.N.AN
RetrocopyNTAMQLVDDPAQFDVMVMPNLYGNIVNNICTGLVGGPGLVPGANYGHKYSLFEAGARHSGKSIANRNLAN
ParentalPTAMLLASCMMLDYLGLHDSAALVRKAILRTMNEHRMHTPDIGGQGTTSEVVQSIIRQI
PTAMLLASC.MLD.L.L...A.L.R.A...........T.D.GG...T..V..S...QI
RetrocopyPTAMLLASCLMLDHLELKEYAWLIRNAAIKSIGDLKIQTVDLGGSASTTDVIHSVLNQI

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
DRP000627_gill 0 .00 RPM 8 .06 RPM
DRP000627_kidney 0 .00 RPM 7 .41 RPM
DRP000627_pectoral_fin 0 .00 RPM 11 .18 RPM
DRP000627_pelvic_fin 0 .00 RPM 16 .44 RPM
DRP000627_pharynx 0 .00 RPM 6 .73 RPM
DRP000627_tail_muscle 0 .00 RPM 7 .19 RPM

ChIP-Seq - click to see more details

Latimeria chalumnae was not studied using ChIP-Seq data.

EST - click to see more details

Latimeria chalumnae was not studied using EST data.

TSS - click to see more details

Latimeria chalumnae was not studied using FANTOM5 data.

Lab - click to see more details

retro_lcha_17 was not experimentally validated.

Retrocopy orthology:
Latimeria chalumnae does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.
Parental genes homology:
Parental genes homology involve 23 parental genes, and 23 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,
Dipodomys ordii ENSDORG000000060291 retrocopy
retro_dord_38,
Equus caballus ENSECAG000000185091 retrocopy
retro_ecab_941,
Erinaceus europaeus ENSEEUG000000156251 retrocopy
retro_eeur_248,
Homo sapiens ENSG000000678291 retrocopy
retro_hsap_759,
Latimeria chalumnae ENSLACG00000007365 1 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,
Oryctolagus cuniculus ENSOCUG000000165541 retrocopy
retro_ocun_80,
Otolemur garnettii ENSOGAG000000067351 retrocopy
retro_ogar_25,
Procavia capensis ENSPCAG000000089731 retrocopy
retro_pcap_361,
Pan troglodytes ENSPTRG000000243981 retrocopy
retro_ptro_534,
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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