RetrogeneDB ID:

retro_lcha_15

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH127230.1:240877..241468(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLACG00000006857
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:RHOA
Ensembl ID:ENSLACG00000016941
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_15
ATGGCTGCAATAAGAAAGAAGCTGGTGGTGGTCGGGGATGGTGCATGTGGTAAAACCTGCCTGCTGATTGTCTTCAGCAA
GGACGAGTTCCCCGAGGTGTATGTGCCCACGGTCTTCGAGAACTACGTGGCTGATATCGAGGTGGACGGGAAGCAGGTGG
AGCTGGCGTTGTGGGATACGGCCGGCCAAGAGGACTACGATCGCCTCCGTCCCCTGTCCTATCCGGACACGGACGTCATC
CTGATGTGCTTTTCGGTGGACAGCCCCGACTCCCTGGAGAACATCCCCGAGAAGTGGGTGCCGGAGGTCAAGCACTTCTG
CCCTAACGTGCCCATCATCCTGGTGGCCAACAAGAAGGACCTGAGGAACGACGAGAATGTGAGGAACGAGCTGGCCAGGA
TGAAGCAGGAGCCCGTCAAGACCGAGGACGGCCGGGCCATGGCCGTCAGGATCGGGGCTTATGATTACCTGGAGTGCTCG
GCCAAAACCAAAGACGGGGTGCGGGAAGTCTTTGAAACGGCCACCCGAGCTGCACTGCAAAAGCGATCCAGACCAAGTGG
GGGATGTGTCAACTGCTGTAAAGTATTGTGA

ORF - retro_lcha_15 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 87.43 %
Parental protein coverage: 98.96 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMAAIRKKLVIVGDGACGKTCLLIVFSKDQFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
MAAIRKKLV.VGDGACGKTCLLIVFSKD.FPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
RetrocopyMAAIRKKLVVVGDGACGKTCLLIVFSKDEFPEVYVPTVFENYVADIEVDGKQVELALWDTAGQEDYDRLR
ParentalPLSYPDTDVILMCFSIDSPDSLENIPEKWTPEVKHFCPNVPIILVGNKKDLRNDEHTRRELAKMKQEPVK
PLSYPDTDVILMCFS.DSPDSLENIPEKW.PEVKHFCPNVPIILV.NKKDLRNDE..R.ELA.MKQEPVK
RetrocopyPLSYPDTDVILMCFSVDSPDSLENIPEKWVPEVKHFCPNVPIILVANKKDLRNDENVRNELARMKQEPVK
ParentalPEEGRDMANRIVAFGYMECSAKTKDGVREVFELATRAALQAKRCRKKNGCL
.E.GR.MA.RI.A..Y.ECSAKTKDGVREVFE.ATRAALQ.KR.R...GC.
RetrocopyTEDGRAMAVRIGAYDYLECSAKTKDGVREVFETATRAALQ-KRSRPSGGCV

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 6 .28 RPM 39 .39 RPM
DRP000627_kidney 4 .32 RPM 36 .88 RPM
DRP000627_pectoral_fin 20 .14 RPM 74 .57 RPM
DRP000627_pelvic_fin 26 .35 RPM 114 .97 RPM
DRP000627_pharynx 1 .11 RPM 35 .18 RPM
DRP000627_tail_muscle 1 .47 RPM 40 .62 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_15 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 44 parental genes, and 102 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082971 retrocopy
retro_acar_41,
Ailuropoda melanoleuca ENSAMEG000000125843 retrocopies
retro_amel_101, retro_amel_1515, retro_amel_615,
Anas platyrhynchos ENSAPLG000000146871 retrocopy
retro_apla_10,
Bos taurus ENSBTAG000000042792 retrocopies
retro_btau_206, retro_btau_540,
Canis familiaris ENSCAFG000000230662 retrocopies
retro_cfam_1652, retro_cfam_186,
Callithrix jacchus ENSCJAG000000039043 retrocopies
retro_cjac_1306, retro_cjac_2010, retro_cjac_411,
Cavia porcellus ENSCPOG000000140731 retrocopy
retro_cpor_514,
Dasypus novemcinctus ENSDNOG000000128256 retrocopies
retro_dnov_1012, retro_dnov_1814, retro_dnov_1904, retro_dnov_2090, retro_dnov_29, retro_dnov_326,
Dipodomys ordii ENSDORG000000033823 retrocopies
retro_dord_1, retro_dord_18, retro_dord_538,
Erinaceus europaeus ENSEEUG000000130631 retrocopy
retro_eeur_147,
Felis catus ENSFCAG000000274561 retrocopy
retro_fcat_29,
Homo sapiens ENSG000000675602 retrocopies
retro_hsap_108, retro_hsap_3632,
Gasterosteus aculeatus ENSGACG000000056701 retrocopy
retro_gacu_9,
Gallus gallus ENSGALG000000038061 retrocopy
retro_ggal_5,
Gorilla gorilla ENSGGOG000000128431 retrocopy
retro_ggor_2450,
Gadus morhua ENSGMOG000000081881 retrocopy
retro_gmor_18,
Latimeria chalumnae ENSLACG00000016941 1 retrocopy
retro_lcha_15 ,
Loxodonta africana ENSLAFG000000097268 retrocopies
retro_lafr_1196, retro_lafr_1197, retro_lafr_1198, retro_lafr_178, retro_lafr_203, retro_lafr_261, retro_lafr_392, retro_lafr_82,
Meleagris gallopavo ENSMGAG000000022801 retrocopy
retro_mgal_2,
Myotis lucifugus ENSMLUG000000139116 retrocopies
retro_mluc_108, retro_mluc_193, retro_mluc_1976, retro_mluc_2553, retro_mluc_2554, retro_mluc_2555,
Macaca mulatta ENSMMUG000000129621 retrocopy
retro_mmul_977,
Monodelphis domestica ENSMODG000000129812 retrocopies
retro_mdom_19, retro_mdom_294,
Mustela putorius furoENSMPUG000000138405 retrocopies
retro_mputfur_1015, retro_mputfur_140, retro_mputfur_1541, retro_mputfur_1588, retro_mputfur_650,
Mus musculus ENSMUSG000000078159 retrocopies
retro_mmus_178, retro_mmus_191, retro_mmus_2041, retro_mmus_2507, retro_mmus_3728, retro_mmus_3729, retro_mmus_3964, retro_mmus_3965, retro_mmus_3966,
Nomascus leucogenys ENSNLEG000000068394 retrocopies
retro_nleu_104, retro_nleu_2207, retro_nleu_377, retro_nleu_814,
Ornithorhynchus anatinus ENSOANG000000138071 retrocopy
retro_oana_7,
Oryctolagus cuniculus ENSOCUG000000133233 retrocopies
retro_ocun_1075, retro_ocun_726, retro_ocun_854,
Otolemur garnettii ENSOGAG000000284891 retrocopy
retro_ogar_2340,
Oreochromis niloticus ENSONIG000000188841 retrocopy
retro_onil_32,
Ochotona princeps ENSOPRG000000096381 retrocopy
retro_opri_590,
Procavia capensis ENSPCAG000000096993 retrocopies
retro_pcap_191, retro_pcap_202, retro_pcap_98,
Pelodiscus sinensis ENSPSIG000000153281 retrocopy
retro_psin_7,
Pan troglodytes ENSPTRG000000149223 retrocopies
retro_ptro_10, retro_ptro_2456, retro_ptro_625,
Pteropus vampyrus ENSPVAG000000087381 retrocopy
retro_pvam_599,
Rattus norvegicus ENSRNOG000000505193 retrocopies
retro_rnor_127, retro_rnor_2899, retro_rnor_408,
Sorex araneus ENSSARG000000085092 retrocopies
retro_sara_137, retro_sara_325,
Sarcophilus harrisii ENSSHAG000000163082 retrocopies
retro_shar_60, retro_shar_96,
Sus scrofa ENSSSCG000000220801 retrocopy
retro_sscr_72,
Ictidomys tridecemlineatus ENSSTOG000000045612 retrocopies
retro_itri_39, retro_itri_96,
Tupaia belangeri ENSTBEG000000024171 retrocopy
retro_tbel_26,
Takifugu rubripes ENSTRUG000000119441 retrocopy
retro_trub_19,
Tarsius syrichta ENSTSYG000000082203 retrocopies
retro_tsyr_1604, retro_tsyr_413, retro_tsyr_593,
Tursiops truncatus ENSTTRG000000173702 retrocopies
retro_ttru_27, retro_ttru_339,
Vicugna pacos ENSVPAG000000109313 retrocopies
retro_vpac_130, retro_vpac_24, retro_vpac_492,


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