RetrogeneDB ID: retro_eeur_27

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_1439:110755..111205(+)
• Located in intron of: ENSEEUG00000003540

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000004394
• Aliases: None
• Description: None

Sequence

>retro_eeur_27
AAGACCATTCTCAGCAACCAGACCGTCGACATCTCTCTGAAGGGCCGCACGGTCATCGTGAAGGGCCCCAGAGGCACCCT
GCGGAGGGACTTCAACCACATCAACGTGGAGCTCAGTCTCCTCGGAAAGAAAAAGAAGCGGCTCCGAGTTGACAAATGGT
GGGGAAATAGAAAGGAACTGGCTTCTGTCCGCATTATCTGCAGCCATGTACAGAACATGATCAAGGGTGTTACACTGGGC
TTCCGATACAAAATGAGGTCCGTGTATGCTCACTTCCCTATCAACGTTGTTATTCAGGAGAATGGGTCTCTTGTTGAAAT
CAGAAACTTCTTGGGAGAAAAATACATACGCAGGGTTTGAATGAGGTCAGGTGTTGCATGCTCACTATCGCAAGCCCAGA
AAGATGAATTAATTCTTGAAGGAAATGACATCGAACTTGTATCAAATTCA

Alignment

ORF - retro_eeur_27 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 95.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTVDIPENVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNRKELATVRTICSHV
          .T......VDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNRKELA.VR.ICSHV
Retrocopy KTILSNQTVDISLKGRTVIVKGPRGTLRRDFNHINVELSLLGKKKKRLRVDKWWGNRKELASVRIICSHV

Parental  QNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRVRMRSGVACSLSQAQKDELILE
          QNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRV.MRSGVACSLSQAQKDELILE
Retrocopy QNMIKGVTLGFRYKMRSVYAHFPINVVIQENGSLVEIRNFLGEKYIRRV*MRSGVACSLSQAQKDELILE

Parental  GNDIELVSNS
          GNDIELVSNS
Retrocopy GNDIELVSNS

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
SRP017611_brain	6.45 RPM	49.63 RPM
SRP017611_kidney	18.19 RPM	96.58 RPM
SRP017611_liver	16.08 RPM	63.67 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_27 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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 545 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000007317	1 retrocopy	retro_acar_163,
Ailuropoda melanoleuca	ENSAMEG00000003187	31 retrocopies	retro_amel_1018, retro_amel_1078, retro_amel_1080, retro_amel_1081, retro_amel_1108, retro_amel_1132, retro_amel_1137, retro_amel_1226, retro_amel_1246, retro_amel_1315, retro_amel_1374, retro_amel_1413, retro_amel_1498, retro_amel_1507, retro_amel_1539, retro_amel_1645, retro_amel_1690, retro_amel_1779, retro_amel_1848, retro_amel_247, retro_amel_256, retro_amel_380, retro_amel_457, retro_amel_652, retro_amel_665, retro_amel_702, retro_amel_727, retro_amel_872, retro_amel_881, retro_amel_951, retro_amel_963,
Bos taurus	ENSBTAG00000014518	3 retrocopies	retro_btau_200, retro_btau_231, retro_btau_51,
Canis familiaris	ENSCAFG00000016008	28 retrocopies	retro_cfam_1044, retro_cfam_1334, retro_cfam_1401, retro_cfam_1455, retro_cfam_1565, retro_cfam_1571, retro_cfam_1610, retro_cfam_1693, retro_cfam_1737, retro_cfam_1809, retro_cfam_1922, retro_cfam_1938, retro_cfam_207, retro_cfam_245, retro_cfam_288, retro_cfam_416, retro_cfam_434, retro_cfam_460, retro_cfam_636, retro_cfam_642, retro_cfam_644, retro_cfam_722, retro_cfam_769, retro_cfam_793, retro_cfam_86, retro_cfam_890, retro_cfam_952, retro_cfam_982,
Callithrix jacchus	ENSCJAG00000000723	29 retrocopies	retro_cjac_1075, retro_cjac_1115, retro_cjac_1335, retro_cjac_1589, retro_cjac_1735, retro_cjac_1780, retro_cjac_1872, retro_cjac_2166, retro_cjac_2549, retro_cjac_2554, retro_cjac_2621, retro_cjac_2637, retro_cjac_2741, retro_cjac_2826, retro_cjac_2847, retro_cjac_3069, retro_cjac_3070, retro_cjac_3103, retro_cjac_3134, retro_cjac_3245, retro_cjac_392, retro_cjac_593, retro_cjac_627, retro_cjac_650, retro_cjac_684, retro_cjac_690, retro_cjac_709, retro_cjac_784, retro_cjac_825,
Cavia porcellus	ENSCPOG00000004543	15 retrocopies	retro_cpor_1037, retro_cpor_1160, retro_cpor_1264, retro_cpor_1400, retro_cpor_1483, retro_cpor_182, retro_cpor_346, retro_cpor_354, retro_cpor_395, retro_cpor_472, retro_cpor_530, retro_cpor_565, retro_cpor_628, retro_cpor_665, retro_cpor_684,
Danio rerio	ENSDARG00000037350	1 retrocopy	retro_drer_18,
Dasypus novemcinctus	ENSDNOG00000007411	18 retrocopies	retro_dnov_1298, retro_dnov_1560, retro_dnov_1684, retro_dnov_1845, retro_dnov_1877, retro_dnov_1936, retro_dnov_2148, retro_dnov_2277, retro_dnov_2624, retro_dnov_2659, retro_dnov_282, retro_dnov_407, retro_dnov_437, retro_dnov_450, retro_dnov_615, retro_dnov_787, retro_dnov_82, retro_dnov_975,
Dipodomys ordii	ENSDORG00000001088	6 retrocopies	retro_dord_276, retro_dord_42, retro_dord_435, retro_dord_604, retro_dord_637, retro_dord_718,
Equus caballus	ENSECAG00000016489	7 retrocopies	retro_ecab_183, retro_ecab_368, retro_ecab_405, retro_ecab_630, retro_ecab_638, retro_ecab_818, retro_ecab_867,
Erinaceus europaeus	ENSEEUG00000004394	39 retrocopies	retro_eeur_11, retro_eeur_136, retro_eeur_153, retro_eeur_162, retro_eeur_184, retro_eeur_191, retro_eeur_229, retro_eeur_246, retro_eeur_27 , retro_eeur_279, retro_eeur_280, retro_eeur_282, retro_eeur_296, retro_eeur_307, retro_eeur_352, retro_eeur_383, retro_eeur_399, retro_eeur_410, retro_eeur_429, retro_eeur_433, retro_eeur_449, retro_eeur_453, retro_eeur_461, retro_eeur_471, retro_eeur_486, retro_eeur_493, retro_eeur_51, retro_eeur_540, retro_eeur_572, retro_eeur_590, retro_eeur_599, retro_eeur_600, retro_eeur_619, retro_eeur_624, retro_eeur_65, retro_eeur_670, retro_eeur_678, retro_eeur_68, retro_eeur_98,
Felis catus	ENSFCAG00000012284	34 retrocopies	retro_fcat_1010, retro_fcat_1076, retro_fcat_1093, retro_fcat_1121, retro_fcat_1183, retro_fcat_1304, retro_fcat_1329, retro_fcat_1531, retro_fcat_1541, retro_fcat_1560, retro_fcat_1597, retro_fcat_160, retro_fcat_1623, retro_fcat_167, retro_fcat_1675, retro_fcat_169, retro_fcat_1700, retro_fcat_1786, retro_fcat_1828, retro_fcat_272, retro_fcat_330, retro_fcat_341, retro_fcat_356, retro_fcat_403, retro_fcat_491, retro_fcat_651, retro_fcat_744, retro_fcat_747, retro_fcat_748, retro_fcat_788, retro_fcat_871, retro_fcat_874, retro_fcat_880, retro_fcat_914,
Homo sapiens	ENSG00000163682	28 retrocopies	retro_hsap_115, retro_hsap_1318, retro_hsap_1344, retro_hsap_1398, retro_hsap_1554, retro_hsap_1585, retro_hsap_1605, retro_hsap_1606, retro_hsap_1717, retro_hsap_1739, retro_hsap_1840, retro_hsap_1864, retro_hsap_1888, retro_hsap_2048, retro_hsap_2326, retro_hsap_2380, retro_hsap_2867, retro_hsap_3008, retro_hsap_321, retro_hsap_3251, retro_hsap_3303, retro_hsap_3604, retro_hsap_3696, retro_hsap_4023, retro_hsap_4793, retro_hsap_666, retro_hsap_773, retro_hsap_802,
Gorilla gorilla	ENSGGOG00000022799	26 retrocopies	retro_ggor_1029, retro_ggor_1084, retro_ggor_1114, retro_ggor_1180, retro_ggor_1204, retro_ggor_1286, retro_ggor_1311, retro_ggor_1328, retro_ggor_1383, retro_ggor_1476, retro_ggor_1805, retro_ggor_1854, retro_ggor_1985, retro_ggor_2148, retro_ggor_219, retro_ggor_2212, retro_ggor_2260, retro_ggor_2431, retro_ggor_2498, retro_ggor_2499, retro_ggor_2700, retro_ggor_347, retro_ggor_392, retro_ggor_577, retro_ggor_641, retro_ggor_660,
Gadus morhua	ENSGMOG00000001002	1 retrocopy	retro_gmor_28,
Loxodonta africana	ENSLAFG00000012021	38 retrocopies	retro_lafr_1009, retro_lafr_1020, retro_lafr_1047, retro_lafr_1095, retro_lafr_1106, retro_lafr_1126, retro_lafr_1145, retro_lafr_1147, retro_lafr_1151, retro_lafr_1174, retro_lafr_1205, retro_lafr_1224, retro_lafr_1225, retro_lafr_1254, retro_lafr_139, retro_lafr_216, retro_lafr_229, retro_lafr_232, retro_lafr_246, retro_lafr_29, retro_lafr_310, retro_lafr_317, retro_lafr_373, retro_lafr_423, retro_lafr_451, retro_lafr_470, retro_lafr_495, retro_lafr_561, retro_lafr_569, retro_lafr_590, retro_lafr_644, retro_lafr_657, retro_lafr_735, retro_lafr_744, retro_lafr_857, retro_lafr_889, retro_lafr_934, retro_lafr_95,
Macropus eugenii	ENSMEUG00000016722	8 retrocopies	retro_meug_1087, retro_meug_1411, retro_meug_1961, retro_meug_22, retro_meug_440, retro_meug_490, retro_meug_650, retro_meug_763,
Microcebus murinus	ENSMICG00000016778	18 retrocopies	retro_mmur_105, retro_mmur_1141, retro_mmur_1183, retro_mmur_1201, retro_mmur_121, retro_mmur_1292, retro_mmur_1418, retro_mmur_1472, retro_mmur_16, retro_mmur_277, retro_mmur_307, retro_mmur_465, retro_mmur_531, retro_mmur_574, retro_mmur_599, retro_mmur_668, retro_mmur_704, retro_mmur_768,
Myotis lucifugus	ENSMLUG00000004597	34 retrocopies	retro_mluc_1028, retro_mluc_1029, retro_mluc_1261, retro_mluc_1269, retro_mluc_127, retro_mluc_1320, retro_mluc_1368, retro_mluc_1380, retro_mluc_1572, retro_mluc_1655, retro_mluc_1704, retro_mluc_1757, retro_mluc_1813, retro_mluc_1858, retro_mluc_1880, retro_mluc_1983, retro_mluc_2041, retro_mluc_2067, retro_mluc_2112, retro_mluc_2119, retro_mluc_220, retro_mluc_2229, retro_mluc_223, retro_mluc_2230, retro_mluc_2370, retro_mluc_2428, retro_mluc_2495, retro_mluc_2611, retro_mluc_293, retro_mluc_461, retro_mluc_533, retro_mluc_648, retro_mluc_75, retro_mluc_895,
Macaca mulatta	ENSMMUG00000008553	22 retrocopies	retro_mmul_1053, retro_mmul_1076, retro_mmul_1097, retro_mmul_1220, retro_mmul_1259, retro_mmul_1272, retro_mmul_1316, retro_mmul_1336, retro_mmul_1404, retro_mmul_1513, retro_mmul_1714, retro_mmul_180, retro_mmul_1924, retro_mmul_2044, retro_mmul_2070, retro_mmul_2167, retro_mmul_2177, retro_mmul_2185, retro_mmul_321, retro_mmul_345, retro_mmul_833, retro_mmul_961,
Monodelphis domestica	ENSMODG00000020553	7 retrocopies	retro_mdom_1026, retro_mdom_1078, retro_mdom_1261, retro_mdom_1352, retro_mdom_1414, retro_mdom_401, retro_mdom_637,
Mus musculus	ENSMUSG00000047215	2 retrocopies	retro_mmus_262, retro_mmus_81,
Nomascus leucogenys	ENSNLEG00000017100	26 retrocopies	retro_nleu_1308, retro_nleu_1400, retro_nleu_1417, retro_nleu_1469, retro_nleu_1700, retro_nleu_1723, retro_nleu_174, retro_nleu_1764, retro_nleu_1829, retro_nleu_2064, retro_nleu_2072, retro_nleu_2223, retro_nleu_2490, retro_nleu_2568, retro_nleu_2634, retro_nleu_2718, retro_nleu_2799, retro_nleu_2832, retro_nleu_367, retro_nleu_400, retro_nleu_410, retro_nleu_610, retro_nleu_660, retro_nleu_707, retro_nleu_755, retro_nleu_806,
Otolemur garnettii	ENSOGAG00000004935	20 retrocopies	retro_ogar_117, retro_ogar_1223, retro_ogar_1471, retro_ogar_1614, retro_ogar_1694, retro_ogar_1807, retro_ogar_1884, retro_ogar_1906, retro_ogar_1933, retro_ogar_2162, retro_ogar_2173, retro_ogar_2806, retro_ogar_3036, retro_ogar_3115, retro_ogar_3276, retro_ogar_329, retro_ogar_429, retro_ogar_864, retro_ogar_886, retro_ogar_963,
Procavia capensis	ENSPCAG00000005834	22 retrocopies	retro_pcap_153, retro_pcap_209, retro_pcap_216, retro_pcap_225, retro_pcap_229, retro_pcap_243, retro_pcap_254, retro_pcap_259, retro_pcap_325, retro_pcap_387, retro_pcap_39, retro_pcap_410, retro_pcap_411, retro_pcap_417, retro_pcap_418, retro_pcap_47, retro_pcap_49, retro_pcap_50, retro_pcap_60, retro_pcap_75, retro_pcap_79, retro_pcap_92,
Pongo abelii	ENSPPYG00000014675	10 retrocopies	retro_pabe_1117, retro_pabe_1157, retro_pabe_1433, retro_pabe_1521, retro_pabe_1523, retro_pabe_162, retro_pabe_2148, retro_pabe_2372, retro_pabe_2695, retro_pabe_3155,
Rattus norvegicus	ENSRNOG00000026716	3 retrocopies	retro_rnor_237, retro_rnor_310, retro_rnor_332,
Sarcophilus harrisii	ENSSHAG00000004918	8 retrocopies	retro_shar_191, retro_shar_192, retro_shar_236, retro_shar_340, retro_shar_359, retro_shar_406, retro_shar_600, retro_shar_607,
Sus scrofa	ENSSSCG00000025192	15 retrocopies	retro_sscr_1018, retro_sscr_1021, retro_sscr_1065, retro_sscr_1091, retro_sscr_1160, retro_sscr_1196, retro_sscr_1199, retro_sscr_272, retro_sscr_316, retro_sscr_411, retro_sscr_826, retro_sscr_886, retro_sscr_920, retro_sscr_921, retro_sscr_972,
Ictidomys tridecemlineatus	ENSSTOG00000002077	13 retrocopies	retro_itri_1106, retro_itri_1182, retro_itri_1328, retro_itri_305, retro_itri_313, retro_itri_339, retro_itri_392, retro_itri_588, retro_itri_663, retro_itri_838, retro_itri_908, retro_itri_914, retro_itri_956,
Tupaia belangeri	ENSTBEG00000006042	18 retrocopies	retro_tbel_1061, retro_tbel_142, retro_tbel_1761, retro_tbel_18, retro_tbel_1852, retro_tbel_2152, retro_tbel_28, retro_tbel_2902, retro_tbel_2937, retro_tbel_30, retro_tbel_325, retro_tbel_340, retro_tbel_3744, retro_tbel_4288, retro_tbel_44, retro_tbel_4430, retro_tbel_4492, retro_tbel_995,
Tursiops truncatus	ENSTTRG00000014289	13 retrocopies	retro_ttru_1019, retro_ttru_1067, retro_ttru_1116, retro_ttru_1179, retro_ttru_1242, retro_ttru_1250, retro_ttru_1354, retro_ttru_1386, retro_ttru_283, retro_ttru_500, retro_ttru_60, retro_ttru_653, retro_ttru_910,
Vicugna pacos	ENSVPAG00000002023	1 retrocopy	retro_vpac_11,