RetrogeneDB ID:

retro_lcha_45

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH126873.1:45236..45449(+)
Located in intron of:ENSLACG00000000113
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:None
Ensembl ID:ENSLACG00000008511
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_45
ACAGTAAAAACGACATCGCTCAAATTTAAACTGGGGAGGAATTCGATGAAACCACACCGGATGACAGGAAAATGAAGACC
ATCATTAAACTGGAAGATGGTAAACTAATTCAAGTACAGAAGTGGGGATGGAAAAGAGACCACCATAGCAAGGGAACTGA
AAGATGGCAAAATGATTACGACCTGTACCTTGGGTGATATTGTCTGCACAAGG

ORF - retro_lcha_45 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 79.45 %
Parental protein coverage: 52.99 %
Number of stop codons detected: 0
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalTVKTTSVTFKLG-EEFDETTADDRKTKTVFNLENGKLIQVQKW-DGKETIIGRELKDGKMITVCTMGDVV
TVKTTS..FKLG.EEFDETT.DDRK.KT...LE.GKLIQVQKW.DGKET.I.RELKDGKMIT.CT.GD.V
RetrocopyTVKTTSLKFKLG<EEFDETTPDDRKMKTIIKLEDGKLIQVQKW>DGKETTIARELKDGKMITTCTLGDIV
ParentalCTR
CTR
RetrocopyCTR

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 0 .12 RPM
DRP000627_kidney 0 .00 RPM 0 .04 RPM
DRP000627_pectoral_fin 0 .00 RPM 0 .06 RPM
DRP000627_pelvic_fin 0 .00 RPM 0 .11 RPM
DRP000627_pharynx 0 .00 RPM 0 .06 RPM
DRP000627_tail_muscle 0 .00 RPM 0 .02 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_45 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 42 parental genes, and 130 retrocopies.

Species Parental gene accession Retrocopies number
Anolis carolinensis ENSACAG000000135641 retrocopy
retro_acar_190,
Ailuropoda melanoleuca ENSAMEG000000145541 retrocopy
retro_amel_945,
Ailuropoda melanoleuca ENSAMEG000000146191 retrocopy
retro_amel_1139,
Bos taurus ENSBTAG000000473303 retrocopies
retro_btau_1312, retro_btau_1828, retro_btau_886,
Canis familiaris ENSCAFG000000254103 retrocopies
retro_cfam_132, retro_cfam_137, retro_cfam_228,
Callithrix jacchus ENSCJAG000000004331 retrocopy
retro_cjac_2486,
Callithrix jacchus ENSCJAG000000004444 retrocopies
retro_cjac_1832, retro_cjac_2227, retro_cjac_2816, retro_cjac_4084,
Cavia porcellus ENSCPOG000000257321 retrocopy
retro_cpor_948,
Dasypus novemcinctus ENSDNOG000000180665 retrocopies
retro_dnov_1073, retro_dnov_1231, retro_dnov_1318, retro_dnov_2392, retro_dnov_559,
Equus caballus ENSECAG000000082702 retrocopies
retro_ecab_894, retro_ecab_938,
Equus caballus ENSECAG000000235521 retrocopy
retro_ecab_761,
Erinaceus europaeus ENSEEUG000000140232 retrocopies
retro_eeur_405, retro_eeur_627,
Echinops telfairi ENSETEG0000000744314 retrocopies
retro_etel_1024, retro_etel_1241, retro_etel_1276, retro_etel_1405, retro_etel_1467, retro_etel_1706, retro_etel_1842, retro_etel_1904, retro_etel_2003, retro_etel_512, retro_etel_602, retro_etel_620, retro_etel_806, retro_etel_994,
Felis catus ENSFCAG000000060322 retrocopies
retro_fcat_1243, retro_fcat_1834,
Homo sapiens ENSG0000016468712 retrocopies
retro_hsap_1205, retro_hsap_1279, retro_hsap_1520, retro_hsap_1521, retro_hsap_2167, retro_hsap_2568, retro_hsap_3000, retro_hsap_3357, retro_hsap_3376, retro_hsap_3811, retro_hsap_4717, retro_hsap_880,
Homo sapiens ENSG000001974161 retrocopy
retro_hsap_3679,
Gorilla gorilla ENSGGOG000000059648 retrocopies
retro_ggor_1005, retro_ggor_1163, retro_ggor_2079, retro_ggor_2276, retro_ggor_2284, retro_ggor_2563, retro_ggor_2931, retro_ggor_940,
Gorilla gorilla ENSGGOG000000168351 retrocopy
retro_ggor_2488,
Latimeria chalumnae ENSLACG00000008511 3 retrocopies
retro_lcha_37, retro_lcha_45 , retro_lcha_57,
Macropus eugenii ENSMEUG000000021361 retrocopy
retro_meug_1874,
Microcebus murinus ENSMICG000000013112 retrocopies
retro_mmur_137, retro_mmur_702,
Microcebus murinus ENSMICG000000053191 retrocopy
retro_mmur_1131,
Myotis lucifugus ENSMLUG000000095143 retrocopies
retro_mluc_1590, retro_mluc_1920, retro_mluc_501,
Myotis lucifugus ENSMLUG000000095291 retrocopy
retro_mluc_1953,
Macaca mulatta ENSMMUG000000004864 retrocopies
retro_mmul_1417, retro_mmul_1920, retro_mmul_2095, retro_mmul_2230,
Macaca mulatta ENSMMUG000000109061 retrocopy
retro_mmul_1311,
Macaca mulatta ENSMMUG000000193371 retrocopy
retro_mmul_1787,
Mus musculus ENSMUSG000000275334 retrocopies
retro_mmus_1685, retro_mmus_1791, retro_mmus_2084, retro_mmus_3185,
Nomascus leucogenys ENSNLEG000000025151 retrocopy
retro_nleu_528,
Otolemur garnettii ENSOGAG0000000241310 retrocopies
retro_ogar_1024, retro_ogar_1151, retro_ogar_1286, retro_ogar_1676, retro_ogar_2873, retro_ogar_3066, retro_ogar_3099, retro_ogar_3265, retro_ogar_715, retro_ogar_878,
Otolemur garnettii ENSOGAG000000121661 retrocopy
retro_ogar_843,
Oryzias latipes ENSORLG000000082821 retrocopy
retro_olat_7,
Pongo abelii ENSPPYG000000186991 retrocopy
retro_pabe_27,
Pongo abelii ENSPPYG000000187031 retrocopy
retro_pabe_3016,
Pan troglodytes ENSPTRG0000002037312 retrocopies
retro_ptro_1029, retro_ptro_1030, retro_ptro_1498, retro_ptro_1654, retro_ptro_2029, retro_ptro_2131, retro_ptro_2265, retro_ptro_2295, retro_ptro_2664, retro_ptro_3135, retro_ptro_823, retro_ptro_875,
Pan troglodytes ENSPTRG000000226541 retrocopy
retro_ptro_2493,
Pteropus vampyrus ENSPVAG000000178505 retrocopies
retro_pvam_1159, retro_pvam_467, retro_pvam_531, retro_pvam_852, retro_pvam_89,
Rattus norvegicus ENSRNOG000000490753 retrocopies
retro_rnor_1762, retro_rnor_1879, retro_rnor_1997,
Sus scrofa ENSSSCG000000061531 retrocopy
retro_sscr_476,
Ictidomys tridecemlineatus ENSSTOG000000078773 retrocopies
retro_itri_1305, retro_itri_389, retro_itri_72,
Tarsius syrichta ENSTSYG000000014725 retrocopies
retro_tsyr_126, retro_tsyr_1534, retro_tsyr_1894, retro_tsyr_1982, retro_tsyr_2024,
Tursiops truncatus ENSTTRG000000053771 retrocopy
retro_ttru_1800,


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