RetrogeneDB ID: retro_lcha_55

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127017.1:10155..10473(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000001105
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS15A
• Ensembl ID: ENSLACG00000011476
• Aliases: None
• Description: None

Sequence

>retro_lcha_55
TTTAATCCAGCCCTGATCATGGTGCACATGACCATTCTTGCCGATGCTCTTAGGTGCATCAACAATGCAGAGAAATGTGG
GAAGTGCCAGGTTCTTATTTGGCTGTGTTCTAAAATAGTCGTGAGATTCCCATGTGTGATGATGAAGCATGGTTACATTG
GCAAGTTTGAGATGATCAATGATCACAGAGTGGGAAAAATAGTTGTTAACCTCACAGGTAGGCTGAACAAGTGCGGTGTC
ATCAGCCCAAAGTTTGACTGCCAAGGTTTGAGAGATATGGAAAAATGGCAGACTGCGTTGCTGCCTTCACGTCAGTTT

Alignment

ORF - retro_lcha_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.02 %
• Parental protein coverage: 99.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FFPAGIMVRMNVLADALRCINNAEKRGKRQVLIRPCSKVIVRFLCVMMKHGYIGEFEIIDDHRAGKIVVN
          F.PA.IMV.M..LADALRCINNAEK.GK.QVLI..CSK..VRF.CVMMKHGYIG.FE.I.DHR.GKIVVN
Retrocopy FNPALIMVHMTILADALRCINNAEKCGKCQVLIWLCSKIVVRFPCVMMKHGYIGKFEMINDHRVGKIVVN

Parental  LTGRLNKCGVISPRFDCQ-LRDMEKWQTALLPSRQF
          LTGRLNKCGVISP.FDCQ.LRDMEKWQTALLPSRQF
Retrocopy LTGRLNKCGVISPKFDCQGLRDMEKWQTALLPSRQF

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	0.00 RPM	322.27 RPM
DRP000627_kidney	0.00 RPM	333.01 RPM
DRP000627_pectoral_fin	0.00 RPM	470.35 RPM
DRP000627_pelvic_fin	0.00 RPM	508.56 RPM
DRP000627_pharynx	0.00 RPM	271.50 RPM
DRP000627_tail_muscle	0.00 RPM	151.22 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_55 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 32 parental genes, and 529 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011083	18 retrocopies	retro_amel_106, retro_amel_123, retro_amel_1489, retro_amel_1572, retro_amel_1575, retro_amel_1708, retro_amel_1770, retro_amel_1894, retro_amel_245, retro_amel_271, retro_amel_319, retro_amel_438, retro_amel_442, retro_amel_603, retro_amel_648, retro_amel_66, retro_amel_766, retro_amel_96,
Bos taurus	ENSBTAG00000020733	5 retrocopies	retro_btau_14, retro_btau_171, retro_btau_3, retro_btau_57, retro_btau_98,
Choloepus hoffmanni	ENSCHOG00000012210	12 retrocopies	retro_chof_1122, retro_chof_1141, retro_chof_1376, retro_chof_1676, retro_chof_1915, retro_chof_2388, retro_chof_2522, retro_chof_2526, retro_chof_2612, retro_chof_343, retro_chof_448, retro_chof_754,
Callithrix jacchus	ENSCJAG00000020071	6 retrocopies	retro_cjac_120, retro_cjac_128, retro_cjac_170, retro_cjac_231, retro_cjac_359, retro_cjac_80,
Cavia porcellus	ENSCPOG00000021695	12 retrocopies	retro_cpor_1031, retro_cpor_1087, retro_cpor_1103, retro_cpor_1334, retro_cpor_146, retro_cpor_403, retro_cpor_515, retro_cpor_557, retro_cpor_636, retro_cpor_730, retro_cpor_90, retro_cpor_926,
Dasypus novemcinctus	ENSDNOG00000008341	45 retrocopies	retro_dnov_1029, retro_dnov_1031, retro_dnov_1053, retro_dnov_1060, retro_dnov_1079, retro_dnov_1197, retro_dnov_1246, retro_dnov_147, retro_dnov_1598, retro_dnov_1738, retro_dnov_1766, retro_dnov_1794, retro_dnov_1954, retro_dnov_1963, retro_dnov_2002, retro_dnov_2012, retro_dnov_2047, retro_dnov_2119, retro_dnov_2155, retro_dnov_2182, retro_dnov_2206, retro_dnov_2326, retro_dnov_2338, retro_dnov_2355, retro_dnov_2401, retro_dnov_2437, retro_dnov_2458, retro_dnov_2478, retro_dnov_2479, retro_dnov_2492, retro_dnov_2516, retro_dnov_2519, retro_dnov_2655, retro_dnov_2669, retro_dnov_2689, retro_dnov_462, retro_dnov_494, retro_dnov_505, retro_dnov_629, retro_dnov_653, retro_dnov_667, retro_dnov_686, retro_dnov_774, retro_dnov_785, retro_dnov_87,
Dipodomys ordii	ENSDORG00000001557	5 retrocopies	retro_dord_165, retro_dord_455, retro_dord_496, retro_dord_51, retro_dord_582,
Equus caballus	ENSECAG00000019293	2 retrocopies	retro_ecab_114, retro_ecab_485,
Felis catus	ENSFCAG00000010625	11 retrocopies	retro_fcat_125, retro_fcat_1712, retro_fcat_1745, retro_fcat_1951, retro_fcat_1966, retro_fcat_34, retro_fcat_37, retro_fcat_655, retro_fcat_665, retro_fcat_879, retro_fcat_9,
Homo sapiens	ENSG00000134419	37 retrocopies	retro_hsap_1057, retro_hsap_1335, retro_hsap_1411, retro_hsap_1425, retro_hsap_164, retro_hsap_1695, retro_hsap_1769, retro_hsap_1932, retro_hsap_2020, retro_hsap_2087, retro_hsap_2117, retro_hsap_212, retro_hsap_2181, retro_hsap_2459, retro_hsap_2556, retro_hsap_2586, retro_hsap_3044, retro_hsap_3409, retro_hsap_3456, retro_hsap_351, retro_hsap_3514, retro_hsap_3539, retro_hsap_3590, retro_hsap_370, retro_hsap_374, retro_hsap_3904, retro_hsap_3987, retro_hsap_4033, retro_hsap_4071, retro_hsap_4300, retro_hsap_4802, retro_hsap_509, retro_hsap_629, retro_hsap_636, retro_hsap_685, retro_hsap_727, retro_hsap_861,
Gorilla gorilla	ENSGGOG00000026299	32 retrocopies	retro_ggor_109, retro_ggor_1270, retro_ggor_1406, retro_ggor_1532, retro_ggor_1599, retro_ggor_1619, retro_ggor_1631, retro_ggor_1642, retro_ggor_1728, retro_ggor_2242, retro_ggor_2332, retro_ggor_2376, retro_ggor_2390, retro_ggor_248, retro_ggor_2631, retro_ggor_2706, retro_ggor_283, retro_ggor_2874, retro_ggor_2989, retro_ggor_3075, retro_ggor_340, retro_ggor_365, retro_ggor_384, retro_ggor_466, retro_ggor_469, retro_ggor_551, retro_ggor_557, retro_ggor_558, retro_ggor_588, retro_ggor_614, retro_ggor_835, retro_ggor_85,
Gadus morhua	ENSGMOG00000005862	1 retrocopy	retro_gmor_16,
Latimeria chalumnae	ENSLACG00000011476	1 retrocopy	retro_lcha_55 ,
Loxodonta africana	ENSLAFG00000026996	13 retrocopies	retro_lafr_1161, retro_lafr_1201, retro_lafr_210, retro_lafr_236, retro_lafr_247, retro_lafr_309, retro_lafr_323, retro_lafr_356, retro_lafr_571, retro_lafr_613, retro_lafr_629, retro_lafr_759, retro_lafr_956,
Macropus eugenii	ENSMEUG00000003956	14 retrocopies	retro_meug_1163, retro_meug_1214, retro_meug_1344, retro_meug_1582, retro_meug_1675, retro_meug_1803, retro_meug_184, retro_meug_1845, retro_meug_195, retro_meug_2169, retro_meug_340, retro_meug_520, retro_meug_729, retro_meug_809,
Microcebus murinus	ENSMICG00000012241	20 retrocopies	retro_mmur_1007, retro_mmur_1051, retro_mmur_1112, retro_mmur_113, retro_mmur_1256, retro_mmur_1459, retro_mmur_1536, retro_mmur_185, retro_mmur_239, retro_mmur_250, retro_mmur_261, retro_mmur_297, retro_mmur_319, retro_mmur_486, retro_mmur_536, retro_mmur_570, retro_mmur_587, retro_mmur_772, retro_mmur_788, retro_mmur_984,
Myotis lucifugus	ENSMLUG00000005660	15 retrocopies	retro_mluc_1170, retro_mluc_1376, retro_mluc_1408, retro_mluc_1692, retro_mluc_2038, retro_mluc_2242, retro_mluc_2353, retro_mluc_2406, retro_mluc_2465, retro_mluc_2512, retro_mluc_2514, retro_mluc_263, retro_mluc_823, retro_mluc_824, retro_mluc_949,
Macaca mulatta	ENSMMUG00000005593	3 retrocopies	retro_mmul_112, retro_mmul_293, retro_mmul_486,
Monodelphis domestica	ENSMODG00000005920	6 retrocopies	retro_mdom_1147, retro_mdom_1626, retro_mdom_1659, retro_mdom_1852, retro_mdom_717, retro_mdom_83,
Mustela putorius furo	ENSMPUG00000013424	12 retrocopies	retro_mputfur_1022, retro_mputfur_1124, retro_mputfur_1165, retro_mputfur_1296, retro_mputfur_1404, retro_mputfur_1417, retro_mputfur_1505, retro_mputfur_43, retro_mputfur_448, retro_mputfur_589, retro_mputfur_591, retro_mputfur_772,
Mus musculus	ENSMUSG00000008683	29 retrocopies	retro_mmus_1133, retro_mmus_1337, retro_mmus_1863, retro_mmus_2022, retro_mmus_2086, retro_mmus_2108, retro_mmus_2428, retro_mmus_2461, retro_mmus_2515, retro_mmus_2580, retro_mmus_2608, retro_mmus_2609, retro_mmus_2680, retro_mmus_2779, retro_mmus_2842, retro_mmus_3161, retro_mmus_3293, retro_mmus_3304, retro_mmus_3348, retro_mmus_3352, retro_mmus_3442, retro_mmus_3482, retro_mmus_357, retro_mmus_408, retro_mmus_670, retro_mmus_757, retro_mmus_768, retro_mmus_816, retro_mmus_928,
Oryctolagus cuniculus	ENSOCUG00000000179	25 retrocopies	retro_ocun_1018, retro_ocun_1067, retro_ocun_1078, retro_ocun_1154, retro_ocun_1157, retro_ocun_1168, retro_ocun_1181, retro_ocun_1310, retro_ocun_1343, retro_ocun_1384, retro_ocun_1435, retro_ocun_144, retro_ocun_1600, retro_ocun_239, retro_ocun_253, retro_ocun_540, retro_ocun_559, retro_ocun_581, retro_ocun_587, retro_ocun_594, retro_ocun_634, retro_ocun_748, retro_ocun_780, retro_ocun_806, retro_ocun_92,
Otolemur garnettii	ENSOGAG00000013199	14 retrocopies	retro_ogar_102, retro_ogar_1254, retro_ogar_1302, retro_ogar_1361, retro_ogar_1636, retro_ogar_2241, retro_ogar_2361, retro_ogar_269, retro_ogar_2775, retro_ogar_3283, retro_ogar_3367, retro_ogar_563, retro_ogar_712, retro_ogar_87,
Procavia capensis	ENSPCAG00000002934	5 retrocopies	retro_pcap_113, retro_pcap_142, retro_pcap_304, retro_pcap_362, retro_pcap_41,
Pongo abelii	ENSPPYG00000007139	2 retrocopies	retro_pabe_2008, retro_pabe_34,
Pan troglodytes	ENSPTRG00000007823	2 retrocopies	retro_ptro_289, retro_ptro_76,
Pteropus vampyrus	ENSPVAG00000002901	14 retrocopies	retro_pvam_102, retro_pvam_1132, retro_pvam_1238, retro_pvam_1341, retro_pvam_344, retro_pvam_362, retro_pvam_364, retro_pvam_381, retro_pvam_383, retro_pvam_494, retro_pvam_50, retro_pvam_573, retro_pvam_834, retro_pvam_943,
Rattus norvegicus	ENSRNOG00000018320	5 retrocopies	retro_rnor_1808, retro_rnor_2080, retro_rnor_2586, retro_rnor_324, retro_rnor_378,
Sarcophilus harrisii	ENSSHAG00000017293	6 retrocopies	retro_shar_311, retro_shar_555, retro_shar_619, retro_shar_720, retro_shar_736, retro_shar_764,
Ictidomys tridecemlineatus	ENSSTOG00000025222	26 retrocopies	retro_itri_1013, retro_itri_1037, retro_itri_1092, retro_itri_1103, retro_itri_1213, retro_itri_1297, retro_itri_1407, retro_itri_1493, retro_itri_1504, retro_itri_1516, retro_itri_1726, retro_itri_205, retro_itri_255, retro_itri_443, retro_itri_452, retro_itri_475, retro_itri_491, retro_itri_498, retro_itri_536, retro_itri_624, retro_itri_692, retro_itri_716, retro_itri_829, retro_itri_839, retro_itri_844, retro_itri_927,
Tupaia belangeri	ENSTBEG00000013626	86 retrocopies	retro_tbel_1030, retro_tbel_1045, retro_tbel_1051, retro_tbel_1075, retro_tbel_1079, retro_tbel_1087, retro_tbel_1100, retro_tbel_1111, retro_tbel_1118, retro_tbel_1222, retro_tbel_1284, retro_tbel_1371, retro_tbel_1398, retro_tbel_143, retro_tbel_1431, retro_tbel_1436, retro_tbel_1470, retro_tbel_1499, retro_tbel_155, retro_tbel_1561, retro_tbel_1625, retro_tbel_1709, retro_tbel_1800, retro_tbel_1842, retro_tbel_1886, retro_tbel_1970, retro_tbel_1975, retro_tbel_1976, retro_tbel_2318, retro_tbel_235, retro_tbel_2394, retro_tbel_2395, retro_tbel_2403, retro_tbel_2552, retro_tbel_2656, retro_tbel_2686, retro_tbel_2734, retro_tbel_2779, retro_tbel_2794, retro_tbel_2871, retro_tbel_2904, retro_tbel_2909, retro_tbel_2921, retro_tbel_2977, retro_tbel_2982, retro_tbel_299, retro_tbel_2990, retro_tbel_3074, retro_tbel_3087, retro_tbel_3173, retro_tbel_3237, retro_tbel_3419, retro_tbel_3428, retro_tbel_3489, retro_tbel_3498, retro_tbel_3562, retro_tbel_3610, retro_tbel_3657, retro_tbel_3752, retro_tbel_3761, retro_tbel_379, retro_tbel_3791, retro_tbel_382, retro_tbel_3884, retro_tbel_4084, retro_tbel_4195, retro_tbel_4198, retro_tbel_4210, retro_tbel_4550, retro_tbel_4584, retro_tbel_4605, retro_tbel_4626, retro_tbel_4707, retro_tbel_477, retro_tbel_479, retro_tbel_501, retro_tbel_547, retro_tbel_641, retro_tbel_646, retro_tbel_713, retro_tbel_774, retro_tbel_78, retro_tbel_806, retro_tbel_813, retro_tbel_862, retro_tbel_989,
Tarsius syrichta	ENSTSYG00000007627	45 retrocopies	retro_tsyr_1017, retro_tsyr_1024, retro_tsyr_1049, retro_tsyr_1051, retro_tsyr_1151, retro_tsyr_124, retro_tsyr_1240, retro_tsyr_128, retro_tsyr_1336, retro_tsyr_1449, retro_tsyr_1500, retro_tsyr_1517, retro_tsyr_152, retro_tsyr_1562, retro_tsyr_1628, retro_tsyr_1669, retro_tsyr_1808, retro_tsyr_1814, retro_tsyr_184, retro_tsyr_1928, retro_tsyr_1959, retro_tsyr_2041, retro_tsyr_2137, retro_tsyr_2145, retro_tsyr_2164, retro_tsyr_258, retro_tsyr_271, retro_tsyr_274, retro_tsyr_275, retro_tsyr_284, retro_tsyr_289, retro_tsyr_292, retro_tsyr_332, retro_tsyr_420, retro_tsyr_422, retro_tsyr_449, retro_tsyr_538, retro_tsyr_588, retro_tsyr_595, retro_tsyr_630, retro_tsyr_631, retro_tsyr_68, retro_tsyr_687, retro_tsyr_72, retro_tsyr_79,