RetrogeneDB ID: retro_lcha_94

Retrocopy location

• Organism: Coelacanth (Latimeria chalumnae)
• Coordinates: JH127883.1:443419..443747(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: RPL31
• Ensembl ID: ENSLACG00000013603
• Aliases: None
• Description: None

Sequence

>retro_lcha_94
AAAATGACTCCAGCTAAGAAGGGAGGACAGAAGAAGAAGGGCTACCCTGCTATCAGTGAGGTGGTGACAAGGGAATATAC
CATCAATGTGCACAAACATACCCATGGCATGAGCTTCAAGAAGTGTGTTGCCTAAGCACCTAAGGAAATCTGCAAATTTG
TGACAAAGGAGATCAACACACCTGAAGTACACATATTGACACTTGTTTGACCAAGCAGTCTGGTCTAAAGGTGTCAAGAA
TGTTCCATATTGCATTTGTGTGCATTTATCCAGAAAACACAAGGAGGACAAAGACTATCCTAACAAACTATACACTCTGG
TTACCTAT

Alignment

ORF - retro_lcha_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.18 %
• Parental protein coverage: 83.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMAPAKKGGEKKKGRSAINEVVTREYTINIHKRIHGVSFKKRAPRALKEIRKFAMKEMGTPDVRIDTRL-
          KM.PAKKGG.KKKG..AI.EVVTREYTIN.HK..HG.SFKK....A.KEI.KF..KE..TP.V.I.T...
Retrocopy KMTPAKKGGQKKKGYPAISEVVTREYTINVHKHTHGMSFKKCVA*APKEICKFVTKEINTPEVHILTLV>

Parental  NKAVWSKGVRNVPYRIRVRLSRKRNEDEDSPNKLYTLVTY
          ..AVWSKGV.NVPY.I.V.LSRK..ED.D.PNKLYTLVTY
Retrocopy DQAVWSKGVKNVPYCICVHLSRKHKEDKDYPNKLYTLVTY

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	364.42 RPM
DRP000627_kidney	0.00 RPM	338.73 RPM
DRP000627_pectoral_fin	0.00 RPM	530.82 RPM
DRP000627_pelvic_fin	0.00 RPM	582.76 RPM
DRP000627_pharynx	0.00 RPM	263.31 RPM
DRP000627_tail_muscle	0.00 RPM	192.69 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_94 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 33 parental genes, and 537 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007914	1 retrocopy	retro_acar_168,
Ailuropoda melanoleuca	ENSAMEG00000015647	2 retrocopies	retro_amel_12, retro_amel_222,
Bos taurus	ENSBTAG00000019701	9 retrocopies	retro_btau_1043, retro_btau_1100, retro_btau_1553, retro_btau_160, retro_btau_1777, retro_btau_1783, retro_btau_409, retro_btau_524, retro_btau_867,
Cavia porcellus	ENSCPOG00000021031	5 retrocopies	retro_cpor_1184, retro_cpor_170, retro_cpor_190, retro_cpor_341, retro_cpor_366,
Dipodomys ordii	ENSDORG00000015728	3 retrocopies	retro_dord_164, retro_dord_515, retro_dord_770,
Equus caballus	ENSECAG00000024079	13 retrocopies	retro_ecab_1034, retro_ecab_1102, retro_ecab_163, retro_ecab_206, retro_ecab_259, retro_ecab_332, retro_ecab_397, retro_ecab_414, retro_ecab_448, retro_ecab_451, retro_ecab_499, retro_ecab_812, retro_ecab_972,
Felis catus	ENSFCAG00000026430	13 retrocopies	retro_fcat_1420, retro_fcat_148, retro_fcat_17, retro_fcat_190, retro_fcat_1957, retro_fcat_2003, retro_fcat_251, retro_fcat_46, retro_fcat_466, retro_fcat_658, retro_fcat_725, retro_fcat_803, retro_fcat_881,
Homo sapiens	ENSG00000071082	45 retrocopies	retro_hsap_1026, retro_hsap_1056, retro_hsap_1075, retro_hsap_1102, retro_hsap_1118, retro_hsap_1150, retro_hsap_1217, retro_hsap_1269, retro_hsap_1345, retro_hsap_1527, retro_hsap_1691, retro_hsap_1856, retro_hsap_1865, retro_hsap_1993, retro_hsap_1998, retro_hsap_2215, retro_hsap_2246, retro_hsap_2388, retro_hsap_2470, retro_hsap_2510, retro_hsap_2610, retro_hsap_2615, retro_hsap_2627, retro_hsap_2839, retro_hsap_2921, retro_hsap_2959, retro_hsap_3108, retro_hsap_3325, retro_hsap_3471, retro_hsap_3472, retro_hsap_3525, retro_hsap_3731, retro_hsap_3777, retro_hsap_3788, retro_hsap_3899, retro_hsap_3965, retro_hsap_4070, retro_hsap_4210, retro_hsap_461, retro_hsap_4693, retro_hsap_506, retro_hsap_548, retro_hsap_677, retro_hsap_794, retro_hsap_831,
Gorilla gorilla	ENSGGOG00000006432	24 retrocopies	retro_ggor_1047, retro_ggor_113, retro_ggor_1442, retro_ggor_169, retro_ggor_1811, retro_ggor_1839, retro_ggor_192, retro_ggor_1971, retro_ggor_21, retro_ggor_2132, retro_ggor_2383, retro_ggor_2541, retro_ggor_2547, retro_ggor_2625, retro_ggor_2820, retro_ggor_442, retro_ggor_583, retro_ggor_655, retro_ggor_834, retro_ggor_84, retro_ggor_849, retro_ggor_874, retro_ggor_88, retro_ggor_997,
Latimeria chalumnae	ENSLACG00000013603	1 retrocopy	retro_lcha_94 ,
Loxodonta africana	ENSLAFG00000027873	12 retrocopies	retro_lafr_118, retro_lafr_187, retro_lafr_20, retro_lafr_245, retro_lafr_307, retro_lafr_56, retro_lafr_663, retro_lafr_703, retro_lafr_710, retro_lafr_778, retro_lafr_885, retro_lafr_926,
Macropus eugenii	ENSMEUG00000000963	8 retrocopies	retro_meug_1083, retro_meug_1433, retro_meug_1731, retro_meug_1741, retro_meug_198, retro_meug_418, retro_meug_588, retro_meug_649,
Microcebus murinus	ENSMICG00000016059	15 retrocopies	retro_mmur_1018, retro_mmur_1028, retro_mmur_1080, retro_mmur_130, retro_mmur_1320, retro_mmur_1369, retro_mmur_1386, retro_mmur_1606, retro_mmur_1617, retro_mmur_476, retro_mmur_506, retro_mmur_538, retro_mmur_639, retro_mmur_796, retro_mmur_996,
Myotis lucifugus	ENSMLUG00000002507	21 retrocopies	retro_mluc_1072, retro_mluc_1135, retro_mluc_1239, retro_mluc_1301, retro_mluc_1406, retro_mluc_1470, retro_mluc_1666, retro_mluc_1678, retro_mluc_1896, retro_mluc_1913, retro_mluc_2028, retro_mluc_2124, retro_mluc_2126, retro_mluc_269, retro_mluc_303, retro_mluc_463, retro_mluc_767, retro_mluc_782, retro_mluc_914, retro_mluc_922, retro_mluc_997,
Macaca mulatta	ENSMMUG00000009873	1 retrocopy	retro_mmul_340,
Monodelphis domestica	ENSMODG00000001704	5 retrocopies	retro_mdom_1052, retro_mdom_1464, retro_mdom_1674, retro_mdom_1720, retro_mdom_1818,
Mustela putorius furo	ENSMPUG00000012197	2 retrocopies	retro_mputfur_50, retro_mputfur_71,
Mus musculus	ENSMUSG00000073702	41 retrocopies	retro_mmus_1054, retro_mmus_1143, retro_mmus_1256, retro_mmus_1419, retro_mmus_1456, retro_mmus_1495, retro_mmus_1507, retro_mmus_1532, retro_mmus_1598, retro_mmus_1670, retro_mmus_1674, retro_mmus_1768, retro_mmus_1823, retro_mmus_1836, retro_mmus_1856, retro_mmus_2054, retro_mmus_2152, retro_mmus_2240, retro_mmus_2278, retro_mmus_2398, retro_mmus_2554, retro_mmus_2603, retro_mmus_2620, retro_mmus_2630, retro_mmus_2658, retro_mmus_2677, retro_mmus_2716, retro_mmus_2821, retro_mmus_2959, retro_mmus_2966, retro_mmus_3186, retro_mmus_3196, retro_mmus_3380, retro_mmus_367, retro_mmus_396, retro_mmus_446, retro_mmus_453, retro_mmus_485, retro_mmus_592, retro_mmus_933, retro_mmus_964,
Nomascus leucogenys	ENSNLEG00000014444	2 retrocopies	retro_nleu_47, retro_nleu_530,
Oryctolagus cuniculus	ENSOCUG00000002392	9 retrocopies	retro_ocun_1070, retro_ocun_1074, retro_ocun_1161, retro_ocun_117, retro_ocun_1366, retro_ocun_206, retro_ocun_64, retro_ocun_941, retro_ocun_99,
Otolemur garnettii	ENSOGAG00000014494	10 retrocopies	retro_ogar_103, retro_ogar_143, retro_ogar_150, retro_ogar_178, retro_ogar_181, retro_ogar_186, retro_ogar_262, retro_ogar_271, retro_ogar_29, retro_ogar_3,
Ochotona princeps	ENSOPRG00000001204	34 retrocopies	retro_opri_1032, retro_opri_1059, retro_opri_1081, retro_opri_1108, retro_opri_1117, retro_opri_113, retro_opri_1176, retro_opri_1177, retro_opri_132, retro_opri_152, retro_opri_179, retro_opri_213, retro_opri_236, retro_opri_259, retro_opri_346, retro_opri_411, retro_opri_435, retro_opri_531, retro_opri_561, retro_opri_572, retro_opri_58, retro_opri_588, retro_opri_602, retro_opri_677, retro_opri_710, retro_opri_744, retro_opri_796, retro_opri_803, retro_opri_804, retro_opri_811, retro_opri_819, retro_opri_909, retro_opri_915, retro_opri_93,
Procavia capensis	ENSPCAG00000004787	10 retrocopies	retro_pcap_121, retro_pcap_125, retro_pcap_152, retro_pcap_228, retro_pcap_230, retro_pcap_266, retro_pcap_33, retro_pcap_378, retro_pcap_401, retro_pcap_413,
Pongo abelii	ENSPPYG00000025870	4 retrocopies	retro_pabe_106, retro_pabe_1635, retro_pabe_168, retro_pabe_895,
Pteropus vampyrus	ENSPVAG00000011716	17 retrocopies	retro_pvam_1131, retro_pvam_1265, retro_pvam_1359, retro_pvam_197, retro_pvam_349, retro_pvam_410, retro_pvam_441, retro_pvam_469, retro_pvam_484, retro_pvam_501, retro_pvam_565, retro_pvam_606, retro_pvam_631, retro_pvam_65, retro_pvam_815, retro_pvam_861, retro_pvam_864,
Rattus norvegicus	ENSRNOG00000013508	8 retrocopies	retro_rnor_101, retro_rnor_152, retro_rnor_1809, retro_rnor_217, retro_rnor_22, retro_rnor_267, retro_rnor_277, retro_rnor_286,
Sarcophilus harrisii	ENSSHAG00000011706	3 retrocopies	retro_shar_190, retro_shar_285, retro_shar_721,
Sus scrofa	ENSSSCG00000008170	4 retrocopies	retro_sscr_1072, retro_sscr_1073, retro_sscr_128, retro_sscr_263,
Sus scrofa	ENSSSCG00000025180	6 retrocopies	retro_sscr_20, retro_sscr_34, retro_sscr_469, retro_sscr_501, retro_sscr_713, retro_sscr_81,
Ictidomys tridecemlineatus	ENSSTOG00000010902	15 retrocopies	retro_itri_1068, retro_itri_1074, retro_itri_1077, retro_itri_1140, retro_itri_1142, retro_itri_1223, retro_itri_1467, retro_itri_1570, retro_itri_1634, retro_itri_1791, retro_itri_1900, retro_itri_298, retro_itri_450, retro_itri_680, retro_itri_76,
Tupaia belangeri	ENSTBEG00000016254	137 retrocopies	retro_tbel_1092, retro_tbel_1129, retro_tbel_115, retro_tbel_1176, retro_tbel_1195, retro_tbel_1226, retro_tbel_1239, retro_tbel_1249, retro_tbel_1254, retro_tbel_1258, retro_tbel_1266, retro_tbel_131, retro_tbel_1310, retro_tbel_1334, retro_tbel_1356, retro_tbel_1368, retro_tbel_1369, retro_tbel_1381, retro_tbel_1402, retro_tbel_1414, retro_tbel_1423, retro_tbel_1437, retro_tbel_1454, retro_tbel_1574, retro_tbel_1593, retro_tbel_1597, retro_tbel_1605, retro_tbel_1611, retro_tbel_1612, retro_tbel_1632, retro_tbel_1768, retro_tbel_1797, retro_tbel_1802, retro_tbel_184, retro_tbel_189, retro_tbel_1890, retro_tbel_1897, retro_tbel_1915, retro_tbel_2024, retro_tbel_2027, retro_tbel_2050, retro_tbel_2069, retro_tbel_2093, retro_tbel_2140, retro_tbel_2159, retro_tbel_2233, retro_tbel_2341, retro_tbel_2359, retro_tbel_2382, retro_tbel_246, retro_tbel_2520, retro_tbel_2531, retro_tbel_2581, retro_tbel_2582, retro_tbel_2614, retro_tbel_2625, retro_tbel_2668, retro_tbel_2692, retro_tbel_2709, retro_tbel_2741, retro_tbel_2789, retro_tbel_2825, retro_tbel_2847, retro_tbel_2930, retro_tbel_2951, retro_tbel_3015, retro_tbel_3028, retro_tbel_3035, retro_tbel_3061, retro_tbel_3077, retro_tbel_3154, retro_tbel_3174, retro_tbel_3222, retro_tbel_3274, retro_tbel_3282, retro_tbel_3292, retro_tbel_3346, retro_tbel_3365, retro_tbel_337, retro_tbel_3378, retro_tbel_3425, retro_tbel_3442, retro_tbel_3484, retro_tbel_3500, retro_tbel_3519, retro_tbel_3578, retro_tbel_3580, retro_tbel_3618, retro_tbel_3637, retro_tbel_3710, retro_tbel_3722, retro_tbel_3745, retro_tbel_3775, retro_tbel_3780, retro_tbel_3794, retro_tbel_3801, retro_tbel_381, retro_tbel_3812, retro_tbel_3846, retro_tbel_3869, retro_tbel_3873, retro_tbel_398, retro_tbel_3982, retro_tbel_3996, retro_tbel_4033, retro_tbel_4069, retro_tbel_4158, retro_tbel_4161, retro_tbel_4174, retro_tbel_4235, retro_tbel_4247, retro_tbel_4286, retro_tbel_4297, retro_tbel_4363, retro_tbel_4374, retro_tbel_461, retro_tbel_4612, retro_tbel_4646, retro_tbel_466, retro_tbel_488, retro_tbel_503, retro_tbel_510, retro_tbel_577, retro_tbel_599, retro_tbel_626, retro_tbel_696, retro_tbel_718, retro_tbel_741, retro_tbel_744, retro_tbel_780, retro_tbel_788, retro_tbel_872, retro_tbel_886, retro_tbel_891, retro_tbel_908, retro_tbel_914, retro_tbel_942,
Tarsius syrichta	ENSTSYG00000005427	33 retrocopies	retro_tsyr_1102, retro_tsyr_117, retro_tsyr_1211, retro_tsyr_1535, retro_tsyr_1610, retro_tsyr_1692, retro_tsyr_1861, retro_tsyr_1912, retro_tsyr_1947, retro_tsyr_2001, retro_tsyr_2026, retro_tsyr_2030, retro_tsyr_2079, retro_tsyr_2089, retro_tsyr_2092, retro_tsyr_2100, retro_tsyr_2105, retro_tsyr_2162, retro_tsyr_239, retro_tsyr_294, retro_tsyr_485, retro_tsyr_551, retro_tsyr_596, retro_tsyr_617, retro_tsyr_635, retro_tsyr_666, retro_tsyr_712, retro_tsyr_754, retro_tsyr_766, retro_tsyr_780, retro_tsyr_785, retro_tsyr_813, retro_tsyr_909,
Tursiops truncatus	ENSTTRG00000016447	24 retrocopies	retro_ttru_1054, retro_ttru_1072, retro_ttru_1102, retro_ttru_1470, retro_ttru_1717, retro_ttru_215, retro_ttru_230, retro_ttru_262, retro_ttru_281, retro_ttru_316, retro_ttru_40, retro_ttru_482, retro_ttru_507, retro_ttru_527, retro_ttru_67, retro_ttru_671, retro_ttru_690, retro_ttru_785, retro_ttru_80, retro_ttru_804, retro_ttru_842, retro_ttru_886, retro_ttru_896, retro_ttru_99,