RetrogeneDB ID:

retro_lcha_10

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH127179.1:543842..544412(+)
Located in intron of:None
Retrocopy
information
Ensembl ID:ENSLACG00000010889
Aliases:None
Status:KNOWN_PROTEIN_CODING
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLACG00000019009
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_10
ATGGGTGTCCTGATGAGTCGAATTTACCAGTCTTTAATGAGCTTCTATGGGCTTCAAGCTAGAGTTCTGATGCTGGGCTT
GGATGCAGCTGGGAAAACCACTCTCCTGTATAAAATGAAGCTGAACGAAGCAGTTACCACCATCCCAACCATCGGCTTCA
ACGTGGAAACAGTGGAGCCCCTCAAGAACGTATCTTTCACGGTCTGGGACGTGGGCGGCCAGACCAGGATCCGAACCCTG
TGGAAGCACTACTTCATGAACACGGACGGGCTGGTCTTCGTGGTGGACAGCGCAGACCCAGAGAGGTTCGAAGAAGCCAG
GCAGGAGCTGGAGGCCATTCTGGACGACGACCAGATGCAACGTGTCCCCTTTGTGATCCTGGCCAACAAGCAGGACCTGC
CCGGGGCCAAGAGACCCTCAGAGCTGGTGGACCTGCTCCGCTTGAGGAAGTTTGTCGGACACGAATGGCATGTGCAAGGG
TGCTGCGCCGTGAACGGGGATGGACTAGTCGAGGGGCTGGAGAGACTGTCCGAGATGGTGAAGCAGTACAAAAAGTCAAG
AGCATTCTAG

ORF - retro_lcha_10 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 56.35 %
Parental protein coverage: 98.34 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalMGSLFAKLFSAFVG--KKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVE-YENISFTVWD
MG.L................R.LM.GLDAAGKTT.LYK.KL.E.VTTIPTIGFNVETVE...N.SFTVWD
RetrocopyMGVLMSRIYQSLMSFYGLQARVLMLGLDAAGKTTLLYKMKLNEAVTTIPTIGFNVETVEPLKNVSFTVWD
ParentalVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVTEAREELAKMLSEDELRDATLLVFANKQDLPNAMNPP
VGGQ..IR.LW.HYF.NT.GL.FVVDS.D.ER..EAR.EL...L..D..........ANKQDLP.A..P.
RetrocopyVGGQTRIRTLWKHYFMNTDGLVFVVDSADPERFEEARQELEAILDDDQMQRVPFVILANKQDLPGAKRPS
ParentalELTDKLGLHALHHHSWYIQATCATSGDGLYEGLDWLSKQLK
EL.D.L.L.....H.W..Q..CA..GDGL.EGL..LS...K
RetrocopyELVDLLRLRKFVGHEWHVQGCCAVNGDGLVEGLERLSEMVK

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 .07 RPM 9 .59 RPM
DRP000627_kidney 0 .14 RPM 6 .15 RPM
DRP000627_pectoral_fin 0 .12 RPM 29 .42 RPM
DRP000627_pelvic_fin 0 .25 RPM 36 .67 RPM
DRP000627_pharynx 0 .03 RPM 4 .04 RPM
DRP000627_tail_muscle 0 .08 RPM 3 .48 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_10 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 66 parental genes, and 138 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000082401 retrocopy
retro_acar_12,
Ailuropoda melanoleuca ENSAMEG000000041841 retrocopy
retro_amel_1639,
Ailuropoda melanoleuca ENSAMEG000000070422 retrocopies
retro_amel_28, retro_amel_70,
Anas platyrhynchos ENSAPLG000000045091 retrocopy
retro_apla_4,
Bos taurus ENSBTAG000000067851 retrocopy
retro_btau_26,
Bos taurus ENSBTAG000000077252 retrocopies
retro_btau_1257, retro_btau_1390,
Canis familiaris ENSCAFG000000087671 retrocopy
retro_cfam_119,
Callithrix jacchus ENSCJAG0000001667110 retrocopies
retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Cavia porcellus ENSCPOG000000211741 retrocopy
retro_cpor_1310,
Cavia porcellus ENSCPOG000000250741 retrocopy
retro_cpor_92,
Ciona savignyi ENSCSAVG000000070111 retrocopy
retro_csav_2,
Dasypus novemcinctus ENSDNOG000000104543 retrocopies
retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Dipodomys ordii ENSDORG000000076034 retrocopies
retro_dord_31, retro_dord_351, retro_dord_409, retro_dord_573,
Equus caballus ENSECAG000000095631 retrocopy
retro_ecab_106,
Erinaceus europaeus ENSEEUG000000046384 retrocopies
retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Ficedula albicollis ENSFALG000000010881 retrocopy
retro_falb_2,
Felis catus ENSFCAG000000000882 retrocopies
retro_fcat_2, retro_fcat_59,
Felis catus ENSFCAG000000293741 retrocopy
retro_fcat_1829,
Homo sapiens ENSG000001342871 retrocopy
retro_hsap_36,
Homo sapiens ENSG000001437613 retrocopies
retro_hsap_1008, retro_hsap_1160, retro_hsap_3763,
Gallus gallus ENSGALG000000053931 retrocopy
retro_ggal_7,
Gorilla gorilla ENSGGOG000000112635 retrocopies
retro_ggor_161, retro_ggor_2531, retro_ggor_3071, retro_ggor_801, retro_ggor_906,
Latimeria chalumnae ENSLACG00000019009 1 retrocopy
retro_lcha_10 ,
Loxodonta africana ENSLAFG000000042071 retrocopy
retro_lafr_115,
Macropus eugenii ENSMEUG000000050727 retrocopies
retro_meug_1036, retro_meug_1117, retro_meug_1857, retro_meug_29, retro_meug_395, retro_meug_616, retro_meug_946,
Microcebus murinus ENSMICG000000175451 retrocopy
retro_mmur_37,
Myotis lucifugus ENSMLUG000000070206 retrocopies
retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Myotis lucifugus ENSMLUG000000298461 retrocopy
retro_mluc_119,
Macaca mulatta ENSMMUG000000027923 retrocopies
retro_mmul_237, retro_mmul_541, retro_mmul_810,
Macaca mulatta ENSMMUG000000069681 retrocopy
retro_mmul_174,
Monodelphis domestica ENSMODG000000138041 retrocopy
retro_mdom_241,
Mustela putorius furoENSMPUG000000147301 retrocopy
retro_mputfur_86,
Mus musculus ENSMUSG000000480761 retrocopy
retro_mmus_1718,
Mus musculus ENSMUSG000000518531 retrocopy
retro_mmus_147,
Mus musculus ENSMUSG000000624211 retrocopy
retro_mmus_2056,
Nomascus leucogenys ENSNLEG000000141373 retrocopies
retro_nleu_210, retro_nleu_227, retro_nleu_2929,
Nomascus leucogenys ENSNLEG000000178592 retrocopies
retro_nleu_1348, retro_nleu_94,
Oryctolagus cuniculus ENSOCUG000000231981 retrocopy
retro_ocun_132,
Oryctolagus cuniculus ENSOCUG000000236452 retrocopies
retro_ocun_1137, retro_ocun_247,
Otolemur garnettii ENSOGAG000000025031 retrocopy
retro_ogar_263,
Otolemur garnettii ENSOGAG000000109744 retrocopies
retro_ogar_2431, retro_ogar_295, retro_ogar_3353, retro_ogar_974,
Ochotona princeps ENSOPRG000000074112 retrocopies
retro_opri_13, retro_opri_3,
Ochotona princeps ENSOPRG000000150632 retrocopies
retro_opri_317, retro_opri_759,
Procavia capensis ENSPCAG000000142022 retrocopies
retro_pcap_15, retro_pcap_23,
Petromyzon marinus ENSPMAG000000005311 retrocopy
retro_pmar_5,
Pongo abelii ENSPPYG000000001483 retrocopies
retro_pabe_3159, retro_pabe_849, retro_pabe_965,
Pongo abelii ENSPPYG000000044731 retrocopy
retro_pabe_126,
Pelodiscus sinensis ENSPSIG000000097671 retrocopy
retro_psin_12,
Pan troglodytes ENSPTRG000000020662 retrocopies
retro_ptro_112, retro_ptro_5,
Pteropus vampyrus ENSPVAG000000046261 retrocopy
retro_pvam_7,
Pteropus vampyrus ENSPVAG000000073831 retrocopy
retro_pvam_1324,
Rattus norvegicus ENSRNOG000000305913 retrocopies
retro_rnor_1268, retro_rnor_1348, retro_rnor_1950,
Rattus norvegicus ENSRNOG000000331551 retrocopy
retro_rnor_272,
Rattus norvegicus ENSRNOG000000480891 retrocopy
retro_rnor_2521,
Sarcophilus harrisii ENSSHAG000000036352 retrocopies
retro_shar_25, retro_shar_364,
Sarcophilus harrisii ENSSHAG000000145993 retrocopies
retro_shar_106, retro_shar_462, retro_shar_725,
Sus scrofa ENSSSCG000000139922 retrocopies
retro_sscr_429, retro_sscr_82,
Ictidomys tridecemlineatus ENSSTOG000000042951 retrocopy
retro_itri_175,
Ictidomys tridecemlineatus ENSSTOG000000092883 retrocopies
retro_itri_1754, retro_itri_273, retro_itri_363,
Ictidomys tridecemlineatus ENSSTOG000000197681 retrocopy
retro_itri_883,
Tupaia belangeri ENSTBEG000000092189 retrocopies
retro_tbel_1943, retro_tbel_2224, retro_tbel_2310, retro_tbel_2358, retro_tbel_2662, retro_tbel_2770, retro_tbel_3103, retro_tbel_4217, retro_tbel_4624,
Taeniopygia guttata ENSTGUG000000002331 retrocopy
retro_tgut_2,
Tetraodon nigroviridis ENSTNIG000000116851 retrocopy
retro_tnig_19,
Tursiops truncatus ENSTTRG000000046981 retrocopy
retro_ttru_1081,
Tursiops truncatus ENSTTRG000000141862 retrocopies
retro_ttru_1679, retro_ttru_347,
Vicugna pacos ENSVPAG000000032244 retrocopies
retro_vpac_281, retro_vpac_328, retro_vpac_6, retro_vpac_78,


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