RetrogeneDB ID: retro_lcha_32

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH126666.1:605027..605511(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLACG00000011473
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL21
• Ensembl ID: ENSLACG00000012678
• Aliases: None
• Description: None

Sequence

>retro_lcha_32
ATGACGAACACAAAGGGTAAGAGAAGAGGTACACGGTACATGTTCTCCAGGCCCTTCCGCAAACATGGAGTTGTTCCTCT
GGCCACATACATGCGCATCTACAAGAAAGGCGATATTGTAGACATCAAGGGCACGGGCACCGTTCAAAAAGGTATGCCTC
ACAAGTGCTACCACGGTAAGACTGGAAGAGTTTTTAATGTTACCCAGCACGCAGTAGGCATTATTGTCAACAAACAGGTC
AAGGGTAAAATTCTTGCGAAGAGGATTAATGTACGAATTGAACACGTCAAACACTCAAAGAGCAGAGAGGGCTTCCTGAA
ATGTGTGAAGGAGAATGAAAGCAAGAAGAGCAAAGCTAAAGCAAAAGGCACTTGGTTTGTGCTCAAGCGCCAGCCTGCTC
AGCCCAGAGAAGCCCACTTTGTCAAAACCAAGGGCGGGCAAGGAGCCAGAACTACTGGAGCCAATTCCTTATGAGTTCAT
GGCA

Alignment

ORF - retro_lcha_32 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGTGTVQKGMPHKCYHGKTGRIFNVTQH
          MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGTGTVQKGMPHKCYHGKTGR.FNVTQH
Retrocopy MTNTKGKRRGTRYMFSRPFRKHGVVPLATYMRIYKKGDIVDIKGTGTVQKGMPHKCYHGKTGRVFNVTQH

Parental  AVGIIVNKQVKGKILAKRINVRIEHVKHSKSRESFLKRVKENESKKSEAKVKGTWFVLKRQPAQ-PREAH
          AVGIIVNKQVKGKILAKRINVRIEHVKHSKSRE.FLK.VKENESKKS.AK.KGTWFVLKRQPAQ.P....
Retrocopy AVGIIVNKQVKGKILAKRINVRIEHVKHSKSREGFLKCVKENESKKSKAKAKGTWFVLKRQPAQ>PEKPT

Parental  FVKTK-GKEPELLEPIPYEFMA
          ..K...GKEPELLEPIPYEFMA
Retrocopy LSKPRAGKEPELLEPIPYEFMA

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	1.36 RPM	377.07 RPM
DRP000627_kidney	0.76 RPM	348.22 RPM
DRP000627_pectoral_fin	14.58 RPM	565.20 RPM
DRP000627_pelvic_fin	3.00 RPM	680.97 RPM
DRP000627_pharynx	1.19 RPM	258.24 RPM
DRP000627_tail_muscle	0.77 RPM	161.67 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_32 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 31 parental genes, and 593 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003169	1 retrocopy	retro_acar_153,
Bos taurus	ENSBTAG00000001648	5 retrocopies	retro_btau_1383, retro_btau_194, retro_btau_209, retro_btau_93, retro_btau_976,
Choloepus hoffmanni	ENSCHOG00000007867	6 retrocopies	retro_chof_1472, retro_chof_1596, retro_chof_2421, retro_chof_2454, retro_chof_266, retro_chof_572,
Callithrix jacchus	ENSCJAG00000019355	1 retrocopy	retro_cjac_152,
Cavia porcellus	ENSCPOG00000008784	3 retrocopies	retro_cpor_2, retro_cpor_26, retro_cpor_41,
Dipodomys ordii	ENSDORG00000002226	15 retrocopies	retro_dord_119, retro_dord_149, retro_dord_152, retro_dord_186, retro_dord_189, retro_dord_203, retro_dord_211, retro_dord_247, retro_dord_285, retro_dord_348, retro_dord_488, retro_dord_493, retro_dord_59, retro_dord_761, retro_dord_768,
Equus caballus	ENSECAG00000010661	5 retrocopies	retro_ecab_16, retro_ecab_24, retro_ecab_39, retro_ecab_88, retro_ecab_90,
Felis catus	ENSFCAG00000006750	1 retrocopy	retro_fcat_64,
Homo sapiens	ENSG00000122026	105 retrocopies	retro_hsap_1007, retro_hsap_1011, retro_hsap_1019, retro_hsap_1032, retro_hsap_1040, retro_hsap_1099, retro_hsap_1107, retro_hsap_1213, retro_hsap_1218, retro_hsap_122, retro_hsap_1280, retro_hsap_1288, retro_hsap_1298, retro_hsap_1379, retro_hsap_1381, retro_hsap_1419, retro_hsap_143, retro_hsap_1430, retro_hsap_1446, retro_hsap_1453, retro_hsap_1505, retro_hsap_1576, retro_hsap_1578, retro_hsap_160, retro_hsap_1600, retro_hsap_1663, retro_hsap_1712, retro_hsap_1723, retro_hsap_1734, retro_hsap_1757, retro_hsap_1805, retro_hsap_1842, retro_hsap_1886, retro_hsap_1904, retro_hsap_1920, retro_hsap_2050, retro_hsap_2088, retro_hsap_2109, retro_hsap_2153, retro_hsap_2178, retro_hsap_2221, retro_hsap_2245, retro_hsap_2258, retro_hsap_2266, retro_hsap_2357, retro_hsap_2442, retro_hsap_252, retro_hsap_2625, retro_hsap_2635, retro_hsap_2655, retro_hsap_2716, retro_hsap_2855, retro_hsap_2876, retro_hsap_2916, retro_hsap_2937, retro_hsap_3037, retro_hsap_3039, retro_hsap_3091, retro_hsap_3094, retro_hsap_3119, retro_hsap_3160, retro_hsap_3185, retro_hsap_3264, retro_hsap_3304, retro_hsap_3375, retro_hsap_3429, retro_hsap_3435, retro_hsap_3521, retro_hsap_3555, retro_hsap_3558, retro_hsap_362, retro_hsap_3628, retro_hsap_3658, retro_hsap_3662, retro_hsap_367, retro_hsap_3688, retro_hsap_3694, retro_hsap_3705, retro_hsap_3747, retro_hsap_3764, retro_hsap_381, retro_hsap_3911, retro_hsap_3945, retro_hsap_3955, retro_hsap_4092, retro_hsap_4193, retro_hsap_424, retro_hsap_4276, retro_hsap_4283, retro_hsap_4286, retro_hsap_4302, retro_hsap_4713, retro_hsap_4733, retro_hsap_496, retro_hsap_503, retro_hsap_563, retro_hsap_573, retro_hsap_582, retro_hsap_626, retro_hsap_654, retro_hsap_738, retro_hsap_752, retro_hsap_819, retro_hsap_900, retro_hsap_965,
Latimeria chalumnae	ENSLACG00000012678	1 retrocopy	retro_lcha_32 ,
Loxodonta africana	ENSLAFG00000003677	11 retrocopies	retro_lafr_1167, retro_lafr_308, retro_lafr_331, retro_lafr_583, retro_lafr_63, retro_lafr_652, retro_lafr_738, retro_lafr_740, retro_lafr_856, retro_lafr_89, retro_lafr_97,
Microcebus murinus	ENSMICG00000014754	54 retrocopies	retro_mmur_1011, retro_mmur_1019, retro_mmur_1078, retro_mmur_1200, retro_mmur_1232, retro_mmur_1276, retro_mmur_1293, retro_mmur_1329, retro_mmur_1337, retro_mmur_1348, retro_mmur_1395, retro_mmur_1448, retro_mmur_1451, retro_mmur_146, retro_mmur_1464, retro_mmur_1524, retro_mmur_1533, retro_mmur_1587, retro_mmur_1598, retro_mmur_1616, retro_mmur_1623, retro_mmur_1632, retro_mmur_177, retro_mmur_234, retro_mmur_251, retro_mmur_296, retro_mmur_310, retro_mmur_328, retro_mmur_385, retro_mmur_405, retro_mmur_418, retro_mmur_434, retro_mmur_437, retro_mmur_438, retro_mmur_478, retro_mmur_489, retro_mmur_539, retro_mmur_541, retro_mmur_547, retro_mmur_627, retro_mmur_645, retro_mmur_655, retro_mmur_719, retro_mmur_73, retro_mmur_774, retro_mmur_790, retro_mmur_801, retro_mmur_805, retro_mmur_847, retro_mmur_865, retro_mmur_867, retro_mmur_869, retro_mmur_94, retro_mmur_964,
Myotis lucifugus	ENSMLUG00000010093	46 retrocopies	retro_mluc_1066, retro_mluc_1079, retro_mluc_1138, retro_mluc_1164, retro_mluc_1171, retro_mluc_1219, retro_mluc_1274, retro_mluc_1279, retro_mluc_1307, retro_mluc_1323, retro_mluc_1379, retro_mluc_1382, retro_mluc_1409, retro_mluc_1413, retro_mluc_1469, retro_mluc_1481, retro_mluc_1525, retro_mluc_162, retro_mluc_1647, retro_mluc_1753, retro_mluc_1803, retro_mluc_1849, retro_mluc_1862, retro_mluc_1929, retro_mluc_1969, retro_mluc_1981, retro_mluc_2044, retro_mluc_2077, retro_mluc_2109, retro_mluc_2121, retro_mluc_2212, retro_mluc_230, retro_mluc_2335, retro_mluc_2338, retro_mluc_2436, retro_mluc_2592, retro_mluc_27, retro_mluc_279, retro_mluc_360, retro_mluc_503, retro_mluc_554, retro_mluc_620, retro_mluc_631, retro_mluc_806, retro_mluc_961, retro_mluc_97,
Macaca mulatta	ENSMMUG00000023368	2 retrocopies	retro_mmul_288, retro_mmul_45,
Macaca mulatta	ENSMMUG00000029574	2 retrocopies	retro_mmul_1289, retro_mmul_219,
Monodelphis domestica	ENSMODG00000008923	1 retrocopy	retro_mdom_156,
Mustela putorius furo	ENSMPUG00000009353	23 retrocopies	retro_mputfur_1083, retro_mputfur_1117, retro_mputfur_1203, retro_mputfur_1342, retro_mputfur_1345, retro_mputfur_1498, retro_mputfur_196, retro_mputfur_208, retro_mputfur_248, retro_mputfur_256, retro_mputfur_310, retro_mputfur_311, retro_mputfur_398, retro_mputfur_580, retro_mputfur_584, retro_mputfur_699, retro_mputfur_700, retro_mputfur_796, retro_mputfur_806, retro_mputfur_903, retro_mputfur_934, retro_mputfur_991, retro_mputfur_992,
Mus musculus	ENSMUSG00000041453	101 retrocopies	retro_mmus_1012, retro_mmus_1046, retro_mmus_1057, retro_mmus_1083, retro_mmus_1123, retro_mmus_1199, retro_mmus_1287, retro_mmus_1354, retro_mmus_1461, retro_mmus_1475, retro_mmus_1529, retro_mmus_1561, retro_mmus_1572, retro_mmus_1596, retro_mmus_1617, retro_mmus_1641, retro_mmus_1644, retro_mmus_17, retro_mmus_1714, retro_mmus_1739, retro_mmus_1762, retro_mmus_1797, retro_mmus_1848, retro_mmus_1860, retro_mmus_1862, retro_mmus_1875, retro_mmus_1897, retro_mmus_1915, retro_mmus_1931, retro_mmus_1936, retro_mmus_1994, retro_mmus_2042, retro_mmus_2049, retro_mmus_2101, retro_mmus_2130, retro_mmus_2176, retro_mmus_2179, retro_mmus_2185, retro_mmus_2214, retro_mmus_2233, retro_mmus_2237, retro_mmus_2238, retro_mmus_2279, retro_mmus_2309, retro_mmus_2312, retro_mmus_2335, retro_mmus_2344, retro_mmus_2395, retro_mmus_2447, retro_mmus_2517, retro_mmus_2567, retro_mmus_2585, retro_mmus_2598, retro_mmus_266, retro_mmus_2662, retro_mmus_2698, retro_mmus_2707, retro_mmus_2778, retro_mmus_2808, retro_mmus_2853, retro_mmus_2874, retro_mmus_2945, retro_mmus_2980, retro_mmus_3035, retro_mmus_3055, retro_mmus_3085, retro_mmus_3103, retro_mmus_3112, retro_mmus_3220, retro_mmus_3252, retro_mmus_3261, retro_mmus_3295, retro_mmus_3318, retro_mmus_3328, retro_mmus_333, retro_mmus_3341, retro_mmus_3446, retro_mmus_3545, retro_mmus_3581, retro_mmus_3712, retro_mmus_397, retro_mmus_400, retro_mmus_401, retro_mmus_598, retro_mmus_601, retro_mmus_606, retro_mmus_663, retro_mmus_734, retro_mmus_735, retro_mmus_758, retro_mmus_782, retro_mmus_806, retro_mmus_835, retro_mmus_862, retro_mmus_883, retro_mmus_918, retro_mmus_932, retro_mmus_940, retro_mmus_957, retro_mmus_993, retro_mmus_998,
Nomascus leucogenys	ENSNLEG00000000327	6 retrocopies	retro_nleu_112, retro_nleu_1144, retro_nleu_26, retro_nleu_713, retro_nleu_95, retro_nleu_951,
Oryctolagus cuniculus	ENSOCUG00000002506	10 retrocopies	retro_ocun_104, retro_ocun_122, retro_ocun_125, retro_ocun_159, retro_ocun_163, retro_ocun_186, retro_ocun_198, retro_ocun_209, retro_ocun_232, retro_ocun_86,
Otolemur garnettii	ENSOGAG00000033936	4 retrocopies	retro_ogar_1787, retro_ogar_2621, retro_ogar_3093, retro_ogar_416,
Otolemur garnettii	ENSOGAG00000034423	1 retrocopy	retro_ogar_3296,
Pongo abelii	ENSPPYG00000005233	7 retrocopies	retro_pabe_1173, retro_pabe_1404, retro_pabe_1437, retro_pabe_3494, retro_pabe_52, retro_pabe_54, retro_pabe_65,
Pongo abelii	ENSPPYG00000006167	2 retrocopies	retro_pabe_1617, retro_pabe_327,
Pan troglodytes	ENSPTRG00000005728	1 retrocopy	retro_ptro_66,
Pteropus vampyrus	ENSPVAG00000000077	82 retrocopies	retro_pvam_1010, retro_pvam_1012, retro_pvam_1013, retro_pvam_1015, retro_pvam_1030, retro_pvam_1038, retro_pvam_1041, retro_pvam_1050, retro_pvam_1073, retro_pvam_1098, retro_pvam_1103, retro_pvam_1106, retro_pvam_1109, retro_pvam_1123, retro_pvam_120, retro_pvam_1210, retro_pvam_1212, retro_pvam_124, retro_pvam_1247, retro_pvam_1248, retro_pvam_1256, retro_pvam_126, retro_pvam_1262, retro_pvam_1281, retro_pvam_1296, retro_pvam_1308, retro_pvam_1377, retro_pvam_1381, retro_pvam_1393, retro_pvam_1425, retro_pvam_1438, retro_pvam_1459, retro_pvam_1468, retro_pvam_170, retro_pvam_195, retro_pvam_223, retro_pvam_226, retro_pvam_253, retro_pvam_256, retro_pvam_26, retro_pvam_286, retro_pvam_318, retro_pvam_319, retro_pvam_329, retro_pvam_374, retro_pvam_408, retro_pvam_412, retro_pvam_416, retro_pvam_452, retro_pvam_489, retro_pvam_492, retro_pvam_495, retro_pvam_555, retro_pvam_569, retro_pvam_570, retro_pvam_589, retro_pvam_662, retro_pvam_693, retro_pvam_707, retro_pvam_731, retro_pvam_740, retro_pvam_760, retro_pvam_763, retro_pvam_768, retro_pvam_772, retro_pvam_791, retro_pvam_811, retro_pvam_820, retro_pvam_821, retro_pvam_825, retro_pvam_826, retro_pvam_833, retro_pvam_836, retro_pvam_839, retro_pvam_860, retro_pvam_885, retro_pvam_915, retro_pvam_916, retro_pvam_937, retro_pvam_946, retro_pvam_965, retro_pvam_985,
Rattus norvegicus	ENSRNOG00000000957	13 retrocopies	retro_rnor_227, retro_rnor_298, retro_rnor_319, retro_rnor_329, retro_rnor_330, retro_rnor_333, retro_rnor_365, retro_rnor_366, retro_rnor_416, retro_rnor_5, retro_rnor_79, retro_rnor_81, retro_rnor_82,
Sorex araneus	ENSSARG00000013129	51 retrocopies	retro_sara_107, retro_sara_112, retro_sara_120, retro_sara_129, retro_sara_133, retro_sara_138, retro_sara_140, retro_sara_155, retro_sara_159, retro_sara_170, retro_sara_187, retro_sara_191, retro_sara_193, retro_sara_206, retro_sara_210, retro_sara_226, retro_sara_252, retro_sara_261, retro_sara_286, retro_sara_301, retro_sara_317, retro_sara_343, retro_sara_350, retro_sara_386, retro_sara_406, retro_sara_426, retro_sara_44, retro_sara_46, retro_sara_48, retro_sara_480, retro_sara_485, retro_sara_50, retro_sara_500, retro_sara_502, retro_sara_513, retro_sara_519, retro_sara_520, retro_sara_562, retro_sara_619, retro_sara_622, retro_sara_642, retro_sara_649, retro_sara_652, retro_sara_673, retro_sara_674, retro_sara_677, retro_sara_698, retro_sara_720, retro_sara_729, retro_sara_754, retro_sara_98,
Sarcophilus harrisii	ENSSHAG00000000845	11 retrocopies	retro_shar_224, retro_shar_446, retro_shar_499, retro_shar_531, retro_shar_534, retro_shar_601, retro_shar_664, retro_shar_67, retro_shar_683, retro_shar_729, retro_shar_757,
Sus scrofa	ENSSSCG00000009303	9 retrocopies	retro_sscr_1144, retro_sscr_1188, retro_sscr_336, retro_sscr_343, retro_sscr_624, retro_sscr_674, retro_sscr_741, retro_sscr_837, retro_sscr_863,
Vicugna pacos	ENSVPAG00000006206	13 retrocopies	retro_vpac_129, retro_vpac_140, retro_vpac_147, retro_vpac_174, retro_vpac_187, retro_vpac_273, retro_vpac_298, retro_vpac_388, retro_vpac_394, retro_vpac_593, retro_vpac_600, retro_vpac_61, retro_vpac_633,