RetrogeneDB ID: retro_lcha_7

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126814.1:964267..964606(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000014113
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: rplp1 (1 of 2)
• Ensembl ID: ENSLACG00000012630
• Aliases: None
• Description: ribosomal protein, large, P1 [Source:ZFIN;Acc:ZDB-GENE-030131-8663]

Sequence

>retro_lcha_7
ATGGCTTCCGTGTCCGAGCTGGCTTGTATTTATTCTGCTCTCATCCTCCACGGCGATGAGGTCACCGTCACGGAGGATAA
AATCAATGCCCTCATCAAGGCTGCTGGAGTGAATGTTGAGCCTTTCTGGCCTAGCCTGTTTGCTAAGGCCCTGTCTAGCA
TTGACATTGGCAGCCTGATCTGTAACGTTGGTGCTGGTGGCCCTGTGGCTGCTGGTAGTGCTCCTGCAGGTGGTGCCCCT
GCTGCTAGTGCTGCGCCAGCTGAAGAAAAGAAGGAAGAGGAGAAGAAGGAAGAATCTGAGGAGTCCGATGATGACATGGG
CTTTGGTCTCTTCGACTAA

Alignment

ORF - retro_lcha_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MASVSELACIYSALILHDDEVTVTEDKINALIKAAGVNVEPFWPSLFAKALSSIDIGSLICNVGAGGPVA
          MASVSELACIYSALILH.DEVTVTEDKINALIKAAGVNVEPFWPSLFAKALSSIDIGSLICNVGAGGPVA
Retrocopy MASVSELACIYSALILHGDEVTVTEDKINALIKAAGVNVEPFWPSLFAKALSSIDIGSLICNVGAGGPVA

Parental  AGSAPAGGAPAASAAPAEEKKEEEKKEESEESDDDMGFGLFD
          AGSAPAGGAPAASAAPAEEKKEEEKKEESEESDDDMGFGLFD
Retrocopy AGSAPAGGAPAASAAPAEEKKEEEKKEESEESDDDMGFGLFD

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
DRP000627_gill	2.55 RPM	385.48 RPM
DRP000627_kidney	2.77 RPM	368.32 RPM
DRP000627_pectoral_fin	8.20 RPM	527.20 RPM
DRP000627_pelvic_fin	4.25 RPM	732.34 RPM
DRP000627_pharynx	1.40 RPM	278.31 RPM
DRP000627_tail_muscle	1.22 RPM	185.38 RPM

ChIP-Seq

Latimeria chalumnae was not studied using ChIP-Seq data.

EST

Latimeria chalumnae was not studied using EST data.

TSS

Latimeria chalumnae was not studied using FANTOM5 data.

Lab

retro_lcha_7 was not experimentally validated.

Homology

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.

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Parental genes homology:

Parental genes homology involve 34 parental genes, and 332 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014251	20 retrocopies	retro_amel_1030, retro_amel_1076, retro_amel_110, retro_amel_1152, retro_amel_1191, retro_amel_128, retro_amel_1343, retro_amel_1345, retro_amel_1354, retro_amel_1428, retro_amel_161, retro_amel_1694, retro_amel_1696, retro_amel_1705, retro_amel_1852, retro_amel_205, retro_amel_316, retro_amel_395, retro_amel_404, retro_amel_769,
Bos taurus	ENSBTAG00000018320	4 retrocopies	retro_btau_1131, retro_btau_1717, retro_btau_186, retro_btau_615,
Choloepus hoffmanni	ENSCHOG00000005944	10 retrocopies	retro_chof_1312, retro_chof_1527, retro_chof_1753, retro_chof_1944, retro_chof_2325, retro_chof_2461, retro_chof_2714, retro_chof_337, retro_chof_666, retro_chof_928,
Callithrix jacchus	ENSCJAG00000032919	19 retrocopies	retro_cjac_1125, retro_cjac_1150, retro_cjac_1222, retro_cjac_1375, retro_cjac_1413, retro_cjac_1666, retro_cjac_1809, retro_cjac_183, retro_cjac_2090, retro_cjac_2626, retro_cjac_267, retro_cjac_2765, retro_cjac_306, retro_cjac_3131, retro_cjac_458, retro_cjac_469, retro_cjac_694, retro_cjac_750, retro_cjac_984,
Cavia porcellus	ENSCPOG00000004321	6 retrocopies	retro_cpor_1011, retro_cpor_1058, retro_cpor_260, retro_cpor_305, retro_cpor_667, retro_cpor_75,
Dasypus novemcinctus	ENSDNOG00000014224	26 retrocopies	retro_dnov_1130, retro_dnov_1325, retro_dnov_1410, retro_dnov_1439, retro_dnov_146, retro_dnov_1467, retro_dnov_1580, retro_dnov_1660, retro_dnov_1667, retro_dnov_17, retro_dnov_1748, retro_dnov_179, retro_dnov_1878, retro_dnov_1911, retro_dnov_1967, retro_dnov_20, retro_dnov_2075, retro_dnov_2234, retro_dnov_240, retro_dnov_2421, retro_dnov_2618, retro_dnov_2640, retro_dnov_405, retro_dnov_561, retro_dnov_601, retro_dnov_746,
Equus caballus	ENSECAG00000008542	4 retrocopies	retro_ecab_380, retro_ecab_677, retro_ecab_820, retro_ecab_958,
Felis catus	ENSFCAG00000032037	23 retrocopies	retro_fcat_1034, retro_fcat_1047, retro_fcat_1089, retro_fcat_1207, retro_fcat_1244, retro_fcat_1436, retro_fcat_1466, retro_fcat_1550, retro_fcat_1580, retro_fcat_1594, retro_fcat_1617, retro_fcat_1797, retro_fcat_1972, retro_fcat_552, retro_fcat_56, retro_fcat_571, retro_fcat_597, retro_fcat_825, retro_fcat_849, retro_fcat_908, retro_fcat_92, retro_fcat_928, retro_fcat_947,
Homo sapiens	ENSG00000137818	18 retrocopies	retro_hsap_1325, retro_hsap_1366, retro_hsap_1719, retro_hsap_1835, retro_hsap_2014, retro_hsap_2079, retro_hsap_2348, retro_hsap_2897, retro_hsap_2936, retro_hsap_3169, retro_hsap_3382, retro_hsap_3392, retro_hsap_3523, retro_hsap_3768, retro_hsap_3939, retro_hsap_472, retro_hsap_533, retro_hsap_679,
Gorilla gorilla	ENSGGOG00000003980	13 retrocopies	retro_ggor_1033, retro_ggor_118, retro_ggor_1276, retro_ggor_1458, retro_ggor_1628, retro_ggor_2036, retro_ggor_2163, retro_ggor_2269, retro_ggor_2381, retro_ggor_2534, retro_ggor_585, retro_ggor_73, retro_ggor_94,
Latimeria chalumnae	ENSLACG00000012630	1 retrocopy	retro_lcha_7 ,
Loxodonta africana	ENSLAFG00000032060	3 retrocopies	retro_lafr_379, retro_lafr_52, retro_lafr_71,
Macropus eugenii	ENSMEUG00000015277	6 retrocopies	retro_meug_1096, retro_meug_1283, retro_meug_1312, retro_meug_1401, retro_meug_1515, retro_meug_793,
Macropus eugenii	ENSMEUG00000015282	2 retrocopies	retro_meug_207, retro_meug_45,
Myotis lucifugus	ENSMLUG00000010542	33 retrocopies	retro_mluc_10, retro_mluc_1064, retro_mluc_1122, retro_mluc_1234, retro_mluc_136, retro_mluc_1374, retro_mluc_1412, retro_mluc_1424, retro_mluc_1654, retro_mluc_1670, retro_mluc_1751, retro_mluc_1810, retro_mluc_1832, retro_mluc_1850, retro_mluc_1944, retro_mluc_197, retro_mluc_2025, retro_mluc_2255, retro_mluc_2265, retro_mluc_2294, retro_mluc_2489, retro_mluc_2578, retro_mluc_433, retro_mluc_472, retro_mluc_570, retro_mluc_577, retro_mluc_61, retro_mluc_732, retro_mluc_791, retro_mluc_858, retro_mluc_916, retro_mluc_945, retro_mluc_95,
Macaca mulatta	ENSMMUG00000014888	7 retrocopies	retro_mmul_111, retro_mmul_2194, retro_mmul_2282, retro_mmul_257, retro_mmul_260, retro_mmul_461, retro_mmul_60,
Monodelphis domestica	ENSMODG00000009209	1 retrocopy	retro_mdom_1022,
Monodelphis domestica	ENSMODG00000009218	4 retrocopies	retro_mdom_1168, retro_mdom_2001, retro_mdom_385, retro_mdom_50,
Mustela putorius furo	ENSMPUG00000000204	13 retrocopies	retro_mputfur_1018, retro_mputfur_113, retro_mputfur_122, retro_mputfur_1265, retro_mputfur_129, retro_mputfur_1334, retro_mputfur_1450, retro_mputfur_1598, retro_mputfur_1613, retro_mputfur_304, retro_mputfur_628, retro_mputfur_635, retro_mputfur_709,
Mustela putorius furo	ENSMPUG00000017096	2 retrocopies	retro_mputfur_1016, retro_mputfur_266,
Mus musculus	ENSMUSG00000007892	6 retrocopies	retro_mmus_180, retro_mmus_206, retro_mmus_2060, retro_mmus_2180, retro_mmus_247, retro_mmus_2525,
Oryctolagus cuniculus	ENSOCUG00000015087	8 retrocopies	retro_ocun_1009, retro_ocun_1464, retro_ocun_1655, retro_ocun_1735, retro_ocun_48, retro_ocun_551, retro_ocun_647, retro_ocun_884,
Otolemur garnettii	ENSOGAG00000029641	19 retrocopies	retro_ogar_1078, retro_ogar_1259, retro_ogar_1363, retro_ogar_1430, retro_ogar_1670, retro_ogar_2215, retro_ogar_2413, retro_ogar_2603, retro_ogar_2683, retro_ogar_2942, retro_ogar_3053, retro_ogar_3222, retro_ogar_3393, retro_ogar_363, retro_ogar_474, retro_ogar_500, retro_ogar_574, retro_ogar_607, retro_ogar_961,
Ochotona princeps	ENSOPRG00000001163	11 retrocopies	retro_opri_1010, retro_opri_130, retro_opri_214, retro_opri_245, retro_opri_38, retro_opri_530, retro_opri_645, retro_opri_768, retro_opri_784, retro_opri_96, retro_opri_972,
Procavia capensis	ENSPCAG00000014595	7 retrocopies	retro_pcap_107, retro_pcap_118, retro_pcap_124, retro_pcap_315, retro_pcap_32, retro_pcap_36, retro_pcap_83,
Pongo abelii	ENSPPYG00000006601	5 retrocopies	retro_pabe_1506, retro_pabe_160, retro_pabe_182, retro_pabe_261, retro_pabe_3080,
Pan troglodytes	ENSPTRG00000007228	1 retrocopy	retro_ptro_96,
Rattus norvegicus	ENSRNOG00000011955	6 retrocopies	retro_rnor_1042, retro_rnor_1402, retro_rnor_1827, retro_rnor_2175, retro_rnor_2678, retro_rnor_493,
Rattus norvegicus	ENSRNOG00000013874	3 retrocopies	retro_rnor_2432, retro_rnor_2700, retro_rnor_2934,
Sarcophilus harrisii	ENSSHAG00000014818	6 retrocopies	retro_shar_182, retro_shar_234, retro_shar_449, retro_shar_550, retro_shar_614, retro_shar_742,
Sus scrofa	ENSSSCG00000004970	16 retrocopies	retro_sscr_1105, retro_sscr_1165, retro_sscr_1184, retro_sscr_1185, retro_sscr_16, retro_sscr_176, retro_sscr_18, retro_sscr_259, retro_sscr_307, retro_sscr_323, retro_sscr_4, retro_sscr_47, retro_sscr_583, retro_sscr_776, retro_sscr_904, retro_sscr_923,
Ictidomys tridecemlineatus	ENSSTOG00000027893	8 retrocopies	retro_itri_1589, retro_itri_1698, retro_itri_1842, retro_itri_1856, retro_itri_226, retro_itri_409, retro_itri_796, retro_itri_976,
Tarsius syrichta	ENSTSYG00000013927	1 retrocopy	retro_tsyr_82,
Tursiops truncatus	ENSTTRG00000013656	20 retrocopies	retro_ttru_1388, retro_ttru_1502, retro_ttru_1645, retro_ttru_1730, retro_ttru_182, retro_ttru_1820, retro_ttru_1826, retro_ttru_227, retro_ttru_266, retro_ttru_28, retro_ttru_389, retro_ttru_553, retro_ttru_626, retro_ttru_666, retro_ttru_679, retro_ttru_687, retro_ttru_711, retro_ttru_755, retro_ttru_768, retro_ttru_803,