RetrogeneDB ID:

retro_lcha_38

Retrocopy
location
Organism:Coelacanth (Latimeria chalumnae)
Coordinates:JH126737.1:1312640..1313017(-)
Located in intron of:ENSLACG00000013728
Retrocopy
information
Ensembl ID:None
Aliases:None
Status:NOVEL
Parental gene
information
Parental gene summary:
Parental gene symbol:RPL17
Ensembl ID:ENSLACG00000008835
Aliases:None
Description:None


Retrocopy-Parental alignment summary:






>retro_lcha_38
AGTGGTGTGGTGGTCAGGTATGCCCAGACGAAGCAGTTTGGTTGGAGACAGGGATGTTGGCCAAAGAAAAGCACTGTGCT
CTTGCTGCACATGCTGAAGAAAGCAAAGGGCAATGCTGAGCTCTAGGGTTTTGGATATCGATTCTCTTATCACCGAGCAC
CTCCATGTGAACAAGGCCCTCAAACTGCACTGATACACTTCCTGTGCTCACGGCCGCATCAACCCTTACATGAGCTCTCC
ACTCTCTTTCTGCACTGAAGGGATCCTAATTGAGAAGGAACAGGTTGCTCCAAAACCAGAAGAGAAAGATTTGTCAAAAA
TCAAAAGGTACTGTATCCCAGAAGAAACTGAAGTAGAAACTCATGTTACAGGAAGAA

ORF - retro_lcha_38 Open Reading Frame is not conserved.
Retrocopy - Parental Gene Alignment summary:
Percent Identity: 60.63 %
Parental protein coverage: 65.76 %
Number of stop codons detected: 3
Number of frameshifts detected 2


Retrocopy - Parental Gene Alignment:

ParentalNGGVGRCAQAKQFGWTQGRWPKKSAEFLLHMLKNAESNAELKG-LDVDSLVIEHIQVNKAPKMRRRTYRA
.G.V.R.AQ.KQFGW.QG.WPKKS...LLHMLK.A..NAEL.G.LD.DSL..EH..VNKA.K....T..A
RetrocopySGVVVRYAQTKQFGWRQGCWPKKSTVLLLHMLKKAKGNAEL*G>LDIDSLITEHLHVNKALKLH*YTSCA
ParentalHGRINPYMSSPCHI--EMILTEKEQIVPKPEE-EVAQKKK--VSQKKLKKQKLMARE
HGRINPYMSSP.....E.IL.EKEQ..PKPEE....QK.K..VSQKKLK.......E
RetrocopyHGRINPYMSSPLSFCTEGILIEKEQVAPKPEE>KICQKSKGTVSQKKLK*KLMLQEE

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 985 .96 RPM
DRP000627_kidney 0 .00 RPM 1175 .75 RPM
DRP000627_pectoral_fin 0 .00 RPM 1430 .83 RPM
DRP000627_pelvic_fin 0 .00 RPM 1387 .46 RPM
DRP000627_pharynx 0 .00 RPM 830 .14 RPM
DRP000627_tail_muscle 0 .00 RPM 570 .10 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_38 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 28 parental genes, and 631 retrocopies.

Species Parental gene accession Retrocopies number
Ailuropoda melanoleuca ENSAMEG0000000949840 retrocopies
retro_amel_1147, retro_amel_1150, retro_amel_1252, retro_amel_1273, retro_amel_132, retro_amel_1422, retro_amel_1435, retro_amel_1487, retro_amel_1541, retro_amel_156, retro_amel_1567, retro_amel_1582, retro_amel_1599, retro_amel_1622, retro_amel_1624, retro_amel_1652, retro_amel_1703, retro_amel_1704, retro_amel_1743, retro_amel_1757, retro_amel_184, retro_amel_1908, retro_amel_1922, retro_amel_208, retro_amel_359, retro_amel_401, retro_amel_425, retro_amel_426, retro_amel_452, retro_amel_486, retro_amel_589, retro_amel_731, retro_amel_736, retro_amel_780, retro_amel_820, retro_amel_834, retro_amel_865, retro_amel_950, retro_amel_953, retro_amel_980,
Bos taurus ENSBTAG000000229025 retrocopies
retro_btau_164, retro_btau_221, retro_btau_4, retro_btau_50, retro_btau_75,
Canis familiaris ENSCAFG000000190447 retrocopies
retro_cfam_102, retro_cfam_171, retro_cfam_175, retro_cfam_189, retro_cfam_2, retro_cfam_239, retro_cfam_34,
Callithrix jacchus ENSCJAG000000047794 retrocopies
retro_cjac_122, retro_cjac_248, retro_cjac_360, retro_cjac_376,
Cavia porcellus ENSCPOG0000001933731 retrocopies
retro_cpor_1004, retro_cpor_1005, retro_cpor_1015, retro_cpor_1050, retro_cpor_1083, retro_cpor_1118, retro_cpor_1125, retro_cpor_1227, retro_cpor_1271, retro_cpor_1305, retro_cpor_1413, retro_cpor_1455, retro_cpor_1539, retro_cpor_159, retro_cpor_213, retro_cpor_238, retro_cpor_272, retro_cpor_319, retro_cpor_374, retro_cpor_50, retro_cpor_521, retro_cpor_662, retro_cpor_675, retro_cpor_776, retro_cpor_784, retro_cpor_792, retro_cpor_827, retro_cpor_872, retro_cpor_924, retro_cpor_943, retro_cpor_955,
Equus caballus ENSECAG000000115479 retrocopies
retro_ecab_162, retro_ecab_331, retro_ecab_488, retro_ecab_584, retro_ecab_620, retro_ecab_678, retro_ecab_751, retro_ecab_939, retro_ecab_977,
Echinops telfairi ENSETEG0000001132210 retrocopies
retro_etel_1787, retro_etel_1810, retro_etel_1900, retro_etel_1936, retro_etel_1954, retro_etel_207, retro_etel_396, retro_etel_470, retro_etel_565, retro_etel_831,
Felis catus ENSFCAG0000001134243 retrocopies
retro_fcat_1002, retro_fcat_1004, retro_fcat_1019, retro_fcat_1050, retro_fcat_1065, retro_fcat_1196, retro_fcat_1235, retro_fcat_1300, retro_fcat_1322, retro_fcat_1426, retro_fcat_1427, retro_fcat_1432, retro_fcat_1516, retro_fcat_1525, retro_fcat_1539, retro_fcat_1552, retro_fcat_1588, retro_fcat_1655, retro_fcat_1692, retro_fcat_1699, retro_fcat_1703, retro_fcat_1740, retro_fcat_1746, retro_fcat_1821, retro_fcat_1864, retro_fcat_1892, retro_fcat_1917, retro_fcat_2023, retro_fcat_211, retro_fcat_264, retro_fcat_360, retro_fcat_461, retro_fcat_481, retro_fcat_488, retro_fcat_532, retro_fcat_607, retro_fcat_734, retro_fcat_791, retro_fcat_808, retro_fcat_855, retro_fcat_900, retro_fcat_917, retro_fcat_988,
Homo sapiens ENSG000002154721 retrocopy
retro_hsap_2367,
Homo sapiens ENSG0000026568133 retrocopies
retro_hsap_1158, retro_hsap_1382, retro_hsap_1423, retro_hsap_1448, retro_hsap_1590, retro_hsap_172, retro_hsap_1728, retro_hsap_1751, retro_hsap_1783, retro_hsap_181, retro_hsap_1893, retro_hsap_1938, retro_hsap_202, retro_hsap_2149, retro_hsap_2398, retro_hsap_2457, retro_hsap_2491, retro_hsap_2582, retro_hsap_2786, retro_hsap_2905, retro_hsap_2933, retro_hsap_295, retro_hsap_3176, retro_hsap_3475, retro_hsap_356, retro_hsap_3620, retro_hsap_3798, retro_hsap_3932, retro_hsap_3943, retro_hsap_3967, retro_hsap_3988, retro_hsap_714, retro_hsap_735,
Gorilla gorilla ENSGGOG000000266971 retrocopy
retro_ggor_167,
Latimeria chalumnae ENSLACG00000008835 1 retrocopy
retro_lcha_38 ,
Loxodonta africana ENSLAFG0000000556916 retrocopies
retro_lafr_1001, retro_lafr_1036, retro_lafr_1060, retro_lafr_1130, retro_lafr_177, retro_lafr_186, retro_lafr_207, retro_lafr_213, retro_lafr_256, retro_lafr_293, retro_lafr_354, retro_lafr_721, retro_lafr_731, retro_lafr_773, retro_lafr_860, retro_lafr_933,
Macropus eugenii ENSMEUG0000001670926 retrocopies
retro_meug_1111, retro_meug_127, retro_meug_1285, retro_meug_1485, retro_meug_1821, retro_meug_188, retro_meug_1886, retro_meug_191, retro_meug_204, retro_meug_2159, retro_meug_2167, retro_meug_2183, retro_meug_257, retro_meug_326, retro_meug_355, retro_meug_373, retro_meug_410, retro_meug_413, retro_meug_509, retro_meug_58, retro_meug_703, retro_meug_738, retro_meug_740, retro_meug_779, retro_meug_81, retro_meug_934,
Myotis lucifugus ENSMLUG0000002555422 retrocopies
retro_mluc_1141, retro_mluc_1224, retro_mluc_1300, retro_mluc_1375, retro_mluc_1468, retro_mluc_1500, retro_mluc_1547, retro_mluc_1579, retro_mluc_1739, retro_mluc_1755, retro_mluc_1822, retro_mluc_1870, retro_mluc_1959, retro_mluc_2018, retro_mluc_2027, retro_mluc_2036, retro_mluc_2059, retro_mluc_2165, retro_mluc_2198, retro_mluc_719, retro_mluc_835, retro_mluc_929,
Myotis lucifugus ENSMLUG0000002926436 retrocopies
retro_mluc_1043, retro_mluc_1060, retro_mluc_1061, retro_mluc_1081, retro_mluc_1094, retro_mluc_1163, retro_mluc_1193, retro_mluc_1206, retro_mluc_123, retro_mluc_1230, retro_mluc_1241, retro_mluc_1416, retro_mluc_157, retro_mluc_1581, retro_mluc_1652, retro_mluc_1677, retro_mluc_1693, retro_mluc_170, retro_mluc_1711, retro_mluc_1848, retro_mluc_1890, retro_mluc_2003, retro_mluc_2064, retro_mluc_2095, retro_mluc_2125, retro_mluc_2387, retro_mluc_2636, retro_mluc_2637, retro_mluc_661, retro_mluc_734, retro_mluc_763, retro_mluc_779, retro_mluc_785, retro_mluc_807, retro_mluc_938, retro_mluc_977,
Macaca mulatta ENSMMUG0000001883726 retrocopies
retro_mmul_1015, retro_mmul_1046, retro_mmul_1205, retro_mmul_1216, retro_mmul_1225, retro_mmul_1441, retro_mmul_163, retro_mmul_172, retro_mmul_1784, retro_mmul_1858, retro_mmul_1952, retro_mmul_2006, retro_mmul_2008, retro_mmul_2257, retro_mmul_2268, retro_mmul_2284, retro_mmul_2304, retro_mmul_2512, retro_mmul_46, retro_mmul_474, retro_mmul_589, retro_mmul_652, retro_mmul_669, retro_mmul_825, retro_mmul_956, retro_mmul_971,
Monodelphis domestica ENSMODG0000000353411 retrocopies
retro_mdom_1153, retro_mdom_1194, retro_mdom_1437, retro_mdom_1734, retro_mdom_1783, retro_mdom_1980, retro_mdom_321, retro_mdom_337, retro_mdom_491, retro_mdom_541, retro_mdom_91,
Mustela putorius furoENSMPUG000000008017 retrocopies
retro_mputfur_1008, retro_mputfur_126, retro_mputfur_1349, retro_mputfur_16, retro_mputfur_184, retro_mputfur_40, retro_mputfur_536,
Mus musculus ENSMUSG0000006232880 retrocopies
retro_mmus_1002, retro_mmus_1004, retro_mmus_1011, retro_mmus_1024, retro_mmus_1032, retro_mmus_1040, retro_mmus_1042, retro_mmus_1087, retro_mmus_1138, retro_mmus_1205, retro_mmus_1208, retro_mmus_1218, retro_mmus_1222, retro_mmus_1226, retro_mmus_1259, retro_mmus_1263, retro_mmus_1308, retro_mmus_1346, retro_mmus_1395, retro_mmus_1404, retro_mmus_1484, retro_mmus_1499, retro_mmus_1502, retro_mmus_1710, retro_mmus_1840, retro_mmus_1842, retro_mmus_1935, retro_mmus_201, retro_mmus_2016, retro_mmus_2034, retro_mmus_2076, retro_mmus_2099, retro_mmus_2124, retro_mmus_2156, retro_mmus_2203, retro_mmus_2261, retro_mmus_2262, retro_mmus_2343, retro_mmus_2345, retro_mmus_243, retro_mmus_2468, retro_mmus_2550, retro_mmus_2613, retro_mmus_2634, retro_mmus_2724, retro_mmus_2759, retro_mmus_2773, retro_mmus_2775, retro_mmus_288, retro_mmus_2919, retro_mmus_3003, retro_mmus_302, retro_mmus_3037, retro_mmus_3049, retro_mmus_310, retro_mmus_311, retro_mmus_314, retro_mmus_327, retro_mmus_334, retro_mmus_3354, retro_mmus_337, retro_mmus_3490, retro_mmus_3601, retro_mmus_3687, retro_mmus_388, retro_mmus_419, retro_mmus_420, retro_mmus_523, retro_mmus_525, retro_mmus_529, retro_mmus_661, retro_mmus_673, retro_mmus_741, retro_mmus_773, retro_mmus_828, retro_mmus_871, retro_mmus_879, retro_mmus_922, retro_mmus_948, retro_mmus_966,
Oryctolagus cuniculus ENSOCUG000000124852 retrocopies
retro_ocun_1433, retro_ocun_231,
Pongo abelii ENSPPYG0000000915143 retrocopies
retro_pabe_1177, retro_pabe_1178, retro_pabe_1179, retro_pabe_1197, retro_pabe_1373, retro_pabe_1408, retro_pabe_1448, retro_pabe_1464, retro_pabe_1531, retro_pabe_1565, retro_pabe_1574, retro_pabe_1725, retro_pabe_1807, retro_pabe_1832, retro_pabe_1902, retro_pabe_2052, retro_pabe_2053, retro_pabe_2088, retro_pabe_2102, retro_pabe_2164, retro_pabe_2231, retro_pabe_2317, retro_pabe_2520, retro_pabe_2635, retro_pabe_2638, retro_pabe_2871, retro_pabe_2917, retro_pabe_2921, retro_pabe_2971, retro_pabe_3020, retro_pabe_3029, retro_pabe_3103, retro_pabe_3187, retro_pabe_3248, retro_pabe_3253, retro_pabe_3262, retro_pabe_3277, retro_pabe_347, retro_pabe_3493, retro_pabe_539, retro_pabe_567, retro_pabe_617, retro_pabe_882,
Pan troglodytes ENSPTRG0000001001251 retrocopies
retro_ptro_1069, retro_ptro_1130, retro_ptro_1193, retro_ptro_1215, retro_ptro_1227, retro_ptro_1267, retro_ptro_1271, retro_ptro_1294, retro_ptro_1308, retro_ptro_1350, retro_ptro_1443, retro_ptro_1509, retro_ptro_161, retro_ptro_1634, retro_ptro_1651, retro_ptro_1653, retro_ptro_1682, retro_ptro_1733, retro_ptro_1790, retro_ptro_183, retro_ptro_1887, retro_ptro_1963, retro_ptro_2059, retro_ptro_2267, retro_ptro_2270, retro_ptro_2355, retro_ptro_2392, retro_ptro_2404, retro_ptro_242, retro_ptro_2450, retro_ptro_2486, retro_ptro_2498, retro_ptro_2515, retro_ptro_2576, retro_ptro_2659, retro_ptro_2675, retro_ptro_2680, retro_ptro_2693, retro_ptro_2706, retro_ptro_2787, retro_ptro_280, retro_ptro_2997, retro_ptro_3073, retro_ptro_490, retro_ptro_509, retro_ptro_523, retro_ptro_719, retro_ptro_793, retro_ptro_948, retro_ptro_973, retro_ptro_985,
Rattus norvegicus ENSRNOG0000001868048 retrocopies
retro_rnor_1028, retro_rnor_1146, retro_rnor_1256, retro_rnor_1281, retro_rnor_1297, retro_rnor_1419, retro_rnor_1469, retro_rnor_1470, retro_rnor_1495, retro_rnor_1504, retro_rnor_1533, retro_rnor_1587, retro_rnor_1603, retro_rnor_1629, retro_rnor_1678, retro_rnor_1856, retro_rnor_1900, retro_rnor_1902, retro_rnor_1911, retro_rnor_1912, retro_rnor_1942, retro_rnor_1980, retro_rnor_2011, retro_rnor_218, retro_rnor_2243, retro_rnor_2348, retro_rnor_242, retro_rnor_2519, retro_rnor_2570, retro_rnor_2572, retro_rnor_2634, retro_rnor_2796, retro_rnor_419, retro_rnor_441, retro_rnor_554, retro_rnor_613, retro_rnor_667, retro_rnor_738, retro_rnor_762, retro_rnor_774, retro_rnor_803, retro_rnor_815, retro_rnor_837, retro_rnor_877, retro_rnor_932, retro_rnor_934, retro_rnor_972, retro_rnor_982,
Sarcophilus harrisii ENSSHAG0000000306014 retrocopies
retro_shar_206, retro_shar_214, retro_shar_279, retro_shar_387, retro_shar_457, retro_shar_586, retro_shar_593, retro_shar_606, retro_shar_713, retro_shar_743, retro_shar_751, retro_shar_800, retro_shar_802, retro_shar_817,
Sus scrofa ENSSSCG0000002964230 retrocopies
retro_sscr_1002, retro_sscr_1003, retro_sscr_1033, retro_sscr_1067, retro_sscr_108, retro_sscr_110, retro_sscr_1106, retro_sscr_111, retro_sscr_1151, retro_sscr_1170, retro_sscr_121, retro_sscr_180, retro_sscr_340, retro_sscr_370, retro_sscr_386, retro_sscr_403, retro_sscr_413, retro_sscr_442, retro_sscr_460, retro_sscr_481, retro_sscr_496, retro_sscr_502, retro_sscr_592, retro_sscr_613, retro_sscr_768, retro_sscr_823, retro_sscr_848, retro_sscr_857, retro_sscr_881, retro_sscr_931,
Ictidomys tridecemlineatus ENSSTOG0000000519333 retrocopies
retro_itri_1006, retro_itri_1015, retro_itri_1066, retro_itri_1070, retro_itri_1148, retro_itri_1212, retro_itri_1238, retro_itri_1312, retro_itri_1351, retro_itri_1360, retro_itri_1385, retro_itri_1424, retro_itri_1451, retro_itri_1476, retro_itri_1479, retro_itri_1625, retro_itri_1648, retro_itri_1712, retro_itri_181, retro_itri_213, retro_itri_300, retro_itri_320, retro_itri_400, retro_itri_425, retro_itri_513, retro_itri_575, retro_itri_601, retro_itri_621, retro_itri_625, retro_itri_708, retro_itri_816, retro_itri_834, retro_itri_949,
Vicugna pacos ENSVPAG000000095681 retrocopy
retro_vpac_10,


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