RetrogeneDB ID:

retro_lcha_53

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH126988.1:78250..78559(-)
Located in intron of:None
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:CALM3
Ensembl ID:ENSLACG00000005059
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_53
TTCAAGGATGCTTTCTCCCTGTTTGCTAAGGATAGCAATGGTACCATCTCCATCATAGAGCTGGGGACAGTGATGAGATC
ACTGGGTCAGAACCCTGCAGAGGCAGAACTTCAGGACATGATCAACGAGGTGGATGCTGAGGGCAATAGACCAATTGTTT
TCCCAGAATTCCTGTCGATGATGGCAAGAAAAATGAAGGACACTGAAAGTGAGGAAGGAATTCGGGAAGCATTCCAAATG
TTTGAGGAAGATGGAAATGGCTACATCAGTGGGGCAGAGTTGTGCCATGTCATGACAGACCTTGGTGAA

ORF - retro_lcha_53 Open Reading Frame is conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 78.64 %
Parental protein coverage: 69.13 %
Number of stop codons detected: 0
Number of frameshifts detected 0


Retrocopy - Parental Gene Alignment:

ParentalFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDS
FK.AFSLF.KD..GTI...ELGTVMRSLGQNP.EAELQDMINEVDA.GN..I.FPEFL.MMARKMKDT.S
RetrocopyFKDAFSLFAKDSNGTISIIELGTVMRSLGQNPAEAELQDMINEVDAEGNRPIVFPEFLSMMARKMKDTES
ParentalEEEIREAFRVFDKDGNGYISAAELRHVMTNLGE
EE.IREAF..F..DGNGYIS.AEL.HVMT.LGE
RetrocopyEEGIREAFQMFEEDGNGYISGAELCHVMTDLGE

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 277 .40 RPM
DRP000627_kidney 0 .00 RPM 257 .52 RPM
DRP000627_pectoral_fin 0 .00 RPM 134 .47 RPM
DRP000627_pelvic_fin 0 .00 RPM 162 .06 RPM
DRP000627_pharynx 0 .00 RPM 427 .20 RPM
DRP000627_tail_muscle 0 .00 RPM 334 .36 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_53 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 59 parental genes, and 188 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000157121 retrocopy
retro_acar_45,
Ailuropoda melanoleuca ENSAMEG000000018014 retrocopies
retro_amel_1215, retro_amel_1714, retro_amel_265, retro_amel_811,
Ailuropoda melanoleuca ENSAMEG000000062042 retrocopies
retro_amel_63, retro_amel_72,
Choloepus hoffmanni ENSCHOG000000082456 retrocopies
retro_chof_1940, retro_chof_2261, retro_chof_367, retro_chof_735, retro_chof_833, retro_chof_965,
Callithrix jacchus ENSCJAG000000006384 retrocopies
retro_cjac_1039, retro_cjac_1401, retro_cjac_2859, retro_cjac_4097,
Callithrix jacchus ENSCJAG000000177403 retrocopies
retro_cjac_1418, retro_cjac_2564, retro_cjac_693,
Cavia porcellus ENSCPOG000000121813 retrocopies
retro_cpor_1012, retro_cpor_87, retro_cpor_89,
Dasypus novemcinctus ENSDNOG000000046459 retrocopies
retro_dnov_1093, retro_dnov_18, retro_dnov_1864, retro_dnov_1972, retro_dnov_2229, retro_dnov_241, retro_dnov_2522, retro_dnov_2674, retro_dnov_865,
Dipodomys ordii ENSDORG000000032006 retrocopies
retro_dord_108, retro_dord_113, retro_dord_201, retro_dord_212, retro_dord_29, retro_dord_5,
Equus caballus ENSECAG000000083964 retrocopies
retro_ecab_15, retro_ecab_59, retro_ecab_750, retro_ecab_882,
Equus caballus ENSECAG000000091621 retrocopy
retro_ecab_279,
Erinaceus europaeus ENSEEUG000000000403 retrocopies
retro_eeur_38, retro_eeur_561, retro_eeur_671,
Echinops telfairi ENSETEG000000093775 retrocopies
retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Echinops telfairi ENSETEG0000001866716 retrocopies
retro_etel_1032, retro_etel_1075, retro_etel_108, retro_etel_1164, retro_etel_1184, retro_etel_1507, retro_etel_1650, retro_etel_1683, retro_etel_1903, retro_etel_2139, retro_etel_22, retro_etel_539, retro_etel_687, retro_etel_864, retro_etel_902, retro_etel_951,
Ficedula albicollis ENSFALG000000128281 retrocopy
retro_falb_16,
Felis catus ENSFCAG000000291415 retrocopies
retro_fcat_1926, retro_fcat_591, retro_fcat_629, retro_fcat_87, retro_fcat_88,
Homo sapiens ENSG000001986682 retrocopies
retro_hsap_1290, retro_hsap_3847,
Gallus gallus ENSGALG000000264451 retrocopy
retro_ggal_9,
Gorilla gorilla ENSGGOG000000285401 retrocopy
retro_ggor_2592,
Gadus morhua ENSGMOG000000093421 retrocopy
retro_gmor_23,
Latimeria chalumnae ENSLACG00000005059 1 retrocopy
retro_lcha_53 ,
Loxodonta africana ENSLAFG000000029051 retrocopy
retro_lafr_1165,
Loxodonta africana ENSLAFG000000098651 retrocopy
retro_lafr_655,
Meleagris gallopavo ENSMGAG000000130551 retrocopy
retro_mgal_13,
Microcebus murinus ENSMICG000000049803 retrocopies
retro_mmur_314, retro_mmur_35, retro_mmur_45,
Myotis lucifugus ENSMLUG000000290166 retrocopies
retro_mluc_13, retro_mluc_1732, retro_mluc_18, retro_mluc_19, retro_mluc_2207, retro_mluc_2258,
Macaca mulatta ENSMMUG000000174661 retrocopy
retro_mmul_256,
Monodelphis domestica ENSMODG000000026964 retrocopies
retro_mdom_137, retro_mdom_178, retro_mdom_185, retro_mdom_208,
Monodelphis domestica ENSMODG000000092221 retrocopy
retro_mdom_1126,
Mustela putorius furoENSMPUG000000080871 retrocopy
retro_mputfur_523,
Mustela putorius furoENSMPUG000000120614 retrocopies
retro_mputfur_1207, retro_mputfur_21, retro_mputfur_838, retro_mputfur_942,
Mus musculus ENSMUSG000000011754 retrocopies
retro_mmus_1519, retro_mmus_2859, retro_mmus_2871, retro_mmus_50,
Nomascus leucogenys ENSNLEG000000169543 retrocopies
retro_nleu_118, retro_nleu_2563, retro_nleu_2862,
Nomascus leucogenys ENSNLEG000000170403 retrocopies
retro_nleu_2039, retro_nleu_2093, retro_nleu_2648,
Ornithorhynchus anatinus ENSOANG000000153651 retrocopy
retro_oana_9,
Oryctolagus cuniculus ENSOCUG000000021072 retrocopies
retro_ocun_1468, retro_ocun_84,
Oryctolagus cuniculus ENSOCUG000000116591 retrocopy
retro_ocun_626,
Otolemur garnettii ENSOGAG000000088246 retrocopies
retro_ogar_1126, retro_ogar_1196, retro_ogar_1432, retro_ogar_1535, retro_ogar_209, retro_ogar_2326,
Otolemur garnettii ENSOGAG000000280891 retrocopy
retro_ogar_1727,
Ochotona princeps ENSOPRG000000154787 retrocopies
retro_opri_1129, retro_opri_1155, retro_opri_16, retro_opri_40, retro_opri_506, retro_opri_830, retro_opri_86,
Petromyzon marinus ENSPMAG000000033231 retrocopy
retro_pmar_12,
Pongo abelii ENSPPYG000000060601 retrocopy
retro_pabe_1045,
Pongo abelii ENSPPYG000000124305 retrocopies
retro_pabe_1068, retro_pabe_1133, retro_pabe_115, retro_pabe_45, retro_pabe_599,
Pelodiscus sinensis ENSPSIG000000131731 retrocopy
retro_psin_9,
Pan troglodytes ENSPTRG000000066261 retrocopy
retro_ptro_3043,
Pan troglodytes ENSPTRG000000119014 retrocopies
retro_ptro_1195, retro_ptro_2623, retro_ptro_83, retro_ptro_881,
Pteropus vampyrus ENSPVAG000000051832 retrocopies
retro_pvam_558, retro_pvam_560,
Pteropus vampyrus ENSPVAG000000100281 retrocopy
retro_pvam_1274,
Rattus norvegicus ENSRNOG000000040603 retrocopies
retro_rnor_318, retro_rnor_389, retro_rnor_392,
Sorex araneus ENSSARG000000087311 retrocopy
retro_sara_119,
Sus scrofa ENSSSCG000000084331 retrocopy
retro_sscr_228,
Sus scrofa ENSSSCG000000257683 retrocopies
retro_sscr_26, retro_sscr_390, retro_sscr_692,
Ictidomys tridecemlineatus ENSSTOG000000218147 retrocopies
retro_itri_1048, retro_itri_1473, retro_itri_37, retro_itri_433, retro_itri_68, retro_itri_778, retro_itri_859,
Tupaia belangeri ENSTBEG0000000056917 retrocopies
retro_tbel_1450, retro_tbel_24, retro_tbel_2418, retro_tbel_258, retro_tbel_2612, retro_tbel_2856, retro_tbel_2933, retro_tbel_3150, retro_tbel_3195, retro_tbel_3956, retro_tbel_4141, retro_tbel_4171, retro_tbel_4212, retro_tbel_4324, retro_tbel_675, retro_tbel_722, retro_tbel_765,
Taeniopygia guttata ENSTGUG000000025811 retrocopy
retro_tgut_6,
Tarsius syrichta ENSTSYG000000125645 retrocopies
retro_tsyr_1641, retro_tsyr_2012, retro_tsyr_2128, retro_tsyr_2148, retro_tsyr_576,
Tursiops truncatus ENSTTRG000000135842 retrocopies
retro_ttru_1637, retro_ttru_1699,
Vicugna pacos ENSVPAG000000045631 retrocopy
retro_vpac_472,
Vicugna pacos ENSVPAG000000092861 retrocopy
retro_vpac_442,


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