RetrogeneDB ID: retro_eeur_679

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_56132:1071..1710(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000010940
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000005292
• Aliases: None
• Description: None

Sequence

>retro_eeur_679
ATCTACATCATCAACTTGAAGAGGACCTGGGAGAAGCTGCTGCTGGCTGCGCGCGCTATTGTTGCCATAGAGAATCCAGC
TGACGTCAGTGTGATCTCTTCCAGGAACACTGGCCAGTGAGCTGTGCTGAAGTTTGCTGCTGCCACTGGAGCCACTCCGA
TTGCTGGTCGCTTCACTCCTGGAACCTTCACTAACCAGATCCAGGCTGCTTTCCGGGAGCCAAGGCTTCTCGTGGTTACT
GACCCCAGGACCGACCACCAGCCTCTCACAGAGGCTTCTTACATTAACCTGCCTACCATCGCTCTGTGTAACACAGACTC
TCTTCTGCGCTATGTAGACATTGCCATTCCCTGCAACAACAAGGGAGCCCACTCAGTGGGTCTCATGTGGTGAATGCTGG
CCCGTGAAGTTCTGCGCTTGCGTGGCACTATCTCCCGTGAACACCCCTGGGAGGTCATGCCTGATCTGTACTTCTACAGA
GATCCTGAGGAGATTGAAAAGGAAGAACAGGCTGCTGCTGAAAAGGCTGTGACCAAGGAGGAGTTCCAGGGCAAATGGAC
GGCTCCAGCCCCAGAATTCACTGCAGCCCAGCCTGAGGTCGCAGACTGGTCTGAGGGCGTGCAGGCACCCTCCGTGCCC

Alignment

ORF - retro_eeur_679 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.24 %
• Parental protein coverage: 85.2 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IYIINLKRTWEKLLLAARAIVAIENPADVSVISSRNTGQRAVLKFAAATGATPIAGRFTPGTFTNQIQAA
          IYIINLKRTWEKLLLAARAIVAIENPADVSVISSRNTGQ.AVLKFAAATGATPIAGRFTPGTFTNQIQAA
Retrocopy IYIINLKRTWEKLLLAARAIVAIENPADVSVISSRNTGQ*AVLKFAAATGATPIAGRFTPGTFTNQIQAA

Parental  FREPRLLVVTDPRADHQPLTEASYVNLPTIALCNTDSPLRYVDIAIPCNNKGAHSVGLMWWMLAREVLRM
          FREPRLLVVTDPR.DHQPLTEASY.NLPTIALCNTDS.LRYVDIAIPCNNKGAHSVGLMW.MLAREVLR.
Retrocopy FREPRLLVVTDPRTDHQPLTEASYINLPTIALCNTDSLLRYVDIAIPCNNKGAHSVGLMW*MLAREVLRL

Parental  RGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGEWTAPAPEFTAAQPEVADWSEGVQVP
          RGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQG.WTAPAPEFTAAQPEVADWSEGVQ.P
Retrocopy RGTISREHPWEVMPDLYFYRDPEEIEKEEQAAAEKAVTKEEFQGKWTAPAPEFTAAQPEVADWSEGVQAP

Parental  SVP
          SVP
Retrocopy SVP

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	66.23 RPM	165.50 RPM
SRP017611_kidney	112.34 RPM	337.76 RPM
SRP017611_liver	77.33 RPM	240.84 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_679 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 24 parental genes, and 349 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000004183	1 retrocopy	retro_acar_140,
Ailuropoda melanoleuca	ENSAMEG00000008962	13 retrocopies	retro_amel_1091, retro_amel_1276, retro_amel_1357, retro_amel_1432, retro_amel_1446, retro_amel_1497, retro_amel_1634, retro_amel_1817, retro_amel_1857, retro_amel_196, retro_amel_430, retro_amel_808, retro_amel_943,
Bos taurus	ENSBTAG00000009757	19 retrocopies	retro_btau_1037, retro_btau_1063, retro_btau_1091, retro_btau_1107, retro_btau_1158, retro_btau_1234, retro_btau_1288, retro_btau_1580, retro_btau_1633, retro_btau_1669, retro_btau_1716, retro_btau_1756, retro_btau_1770, retro_btau_416, retro_btau_848, retro_btau_871, retro_btau_896, retro_btau_964, retro_btau_990,
Canis familiaris	ENSCAFG00000005101	27 retrocopies	retro_cfam_1046, retro_cfam_1109, retro_cfam_1173, retro_cfam_1189, retro_cfam_1263, retro_cfam_1288, retro_cfam_1366, retro_cfam_1373, retro_cfam_1435, retro_cfam_1511, retro_cfam_1534, retro_cfam_1545, retro_cfam_1555, retro_cfam_1679, retro_cfam_1770, retro_cfam_1814, retro_cfam_1957, retro_cfam_1990, retro_cfam_2140, retro_cfam_512, retro_cfam_820, retro_cfam_828, retro_cfam_854, retro_cfam_928, retro_cfam_957, retro_cfam_980, retro_cfam_994,
Cavia porcellus	ENSCPOG00000008715	7 retrocopies	retro_cpor_1206, retro_cpor_1255, retro_cpor_1293, retro_cpor_594, retro_cpor_624, retro_cpor_806, retro_cpor_958,
Dasypus novemcinctus	ENSDNOG00000004048	27 retrocopies	retro_dnov_1022, retro_dnov_108, retro_dnov_1099, retro_dnov_1219, retro_dnov_1372, retro_dnov_1431, retro_dnov_1614, retro_dnov_184, retro_dnov_1913, retro_dnov_1974, retro_dnov_1987, retro_dnov_1988, retro_dnov_2067, retro_dnov_2200, retro_dnov_2224, retro_dnov_2309, retro_dnov_2339, retro_dnov_2469, retro_dnov_2480, retro_dnov_375, retro_dnov_42, retro_dnov_456, retro_dnov_465, retro_dnov_663, retro_dnov_800, retro_dnov_895, retro_dnov_940,
Dipodomys ordii	ENSDORG00000008267	1 retrocopy	retro_dord_548,
Equus caballus	ENSECAG00000013062	5 retrocopies	retro_ecab_193, retro_ecab_453, retro_ecab_46, retro_ecab_592, retro_ecab_71,
Erinaceus europaeus	ENSEEUG00000005292	2 retrocopies	retro_eeur_202, retro_eeur_679 ,
Echinops telfairi	ENSETEG00000018160	4 retrocopies	retro_etel_1399, retro_etel_1665, retro_etel_1960, retro_etel_92,
Felis catus	ENSFCAG00000002739	22 retrocopies	retro_fcat_1119, retro_fcat_1127, retro_fcat_1239, retro_fcat_1353, retro_fcat_1595, retro_fcat_1668, retro_fcat_1694, retro_fcat_1720, retro_fcat_1758, retro_fcat_1804, retro_fcat_1807, retro_fcat_1861, retro_fcat_1970, retro_fcat_239, retro_fcat_258, retro_fcat_384, retro_fcat_391, retro_fcat_551, retro_fcat_682, retro_fcat_722, retro_fcat_793, retro_fcat_906,
Loxodonta africana	ENSLAFG00000032009	5 retrocopies	retro_lafr_1234, retro_lafr_367, retro_lafr_806, retro_lafr_863, retro_lafr_997,
Macropus eugenii	ENSMEUG00000008169	14 retrocopies	retro_meug_1123, retro_meug_1137, retro_meug_1643, retro_meug_1722, retro_meug_1923, retro_meug_1933, retro_meug_1936, retro_meug_343, retro_meug_429, retro_meug_684, retro_meug_810, retro_meug_847, retro_meug_957, retro_meug_990,
Microcebus murinus	ENSMICG00000004518	32 retrocopies	retro_mmur_1031, retro_mmur_1042, retro_mmur_1120, retro_mmur_1310, retro_mmur_1357, retro_mmur_136, retro_mmur_1432, retro_mmur_1482, retro_mmur_1513, retro_mmur_1522, retro_mmur_1593, retro_mmur_1596, retro_mmur_1607, retro_mmur_1628, retro_mmur_196, retro_mmur_219, retro_mmur_284, retro_mmur_302, retro_mmur_367, retro_mmur_477, retro_mmur_522, retro_mmur_532, retro_mmur_559, retro_mmur_561, retro_mmur_604, retro_mmur_620, retro_mmur_714, retro_mmur_727, retro_mmur_753, retro_mmur_756, retro_mmur_821, retro_mmur_933,
Monodelphis domestica	ENSMODG00000010967	2 retrocopies	retro_mdom_1244, retro_mdom_1726,
Mustela putorius furo	ENSMPUG00000002463	21 retrocopies	retro_mputfur_1045, retro_mputfur_1143, retro_mputfur_1194, retro_mputfur_1227, retro_mputfur_1311, retro_mputfur_1318, retro_mputfur_1427, retro_mputfur_1502, retro_mputfur_1558, retro_mputfur_1584, retro_mputfur_288, retro_mputfur_358, retro_mputfur_423, retro_mputfur_477, retro_mputfur_515, retro_mputfur_560, retro_mputfur_576, retro_mputfur_712, retro_mputfur_733, retro_mputfur_932, retro_mputfur_953,
Mus musculus	ENSMUSG00000032518	1 retrocopy	retro_mmus_219,
Ochotona princeps	ENSOPRG00000004505	16 retrocopies	retro_opri_1083, retro_opri_1167, retro_opri_207, retro_opri_223, retro_opri_281, retro_opri_32, retro_opri_362, retro_opri_423, retro_opri_475, retro_opri_483, retro_opri_491, retro_opri_510, retro_opri_518, retro_opri_635, retro_opri_772, retro_opri_874,
Pteropus vampyrus	ENSPVAG00000007794	19 retrocopies	retro_pvam_1189, retro_pvam_1249, retro_pvam_1335, retro_pvam_1403, retro_pvam_1406, retro_pvam_1443, retro_pvam_1446, retro_pvam_396, retro_pvam_499, retro_pvam_532, retro_pvam_548, retro_pvam_60, retro_pvam_635, retro_pvam_650, retro_pvam_789, retro_pvam_889, retro_pvam_896, retro_pvam_898, retro_pvam_98,
Rattus norvegicus	ENSRNOG00000018645	27 retrocopies	retro_rnor_1004, retro_rnor_1114, retro_rnor_1119, retro_rnor_1213, retro_rnor_1301, retro_rnor_1396, retro_rnor_1481, retro_rnor_1634, retro_rnor_1778, retro_rnor_1840, retro_rnor_1886, retro_rnor_2068, retro_rnor_2153, retro_rnor_2329, retro_rnor_2384, retro_rnor_2444, retro_rnor_2553, retro_rnor_2554, retro_rnor_2589, retro_rnor_2637, retro_rnor_2649, retro_rnor_2701, retro_rnor_2810, retro_rnor_2912, retro_rnor_2958, retro_rnor_645, retro_rnor_702,
Sarcophilus harrisii	ENSSHAG00000006896	2 retrocopies	retro_shar_231, retro_shar_484,
Tupaia belangeri	ENSTBEG00000015946	54 retrocopies	retro_tbel_1001, retro_tbel_1007, retro_tbel_1069, retro_tbel_1257, retro_tbel_1303, retro_tbel_1319, retro_tbel_1324, retro_tbel_1354, retro_tbel_1355, retro_tbel_1382, retro_tbel_1395, retro_tbel_1531, retro_tbel_1563, retro_tbel_1616, retro_tbel_1682, retro_tbel_1712, retro_tbel_1723, retro_tbel_1935, retro_tbel_2006, retro_tbel_245, retro_tbel_2511, retro_tbel_2518, retro_tbel_2544, retro_tbel_2735, retro_tbel_2827, retro_tbel_2906, retro_tbel_3198, retro_tbel_3218, retro_tbel_3241, retro_tbel_3272, retro_tbel_3325, retro_tbel_3351, retro_tbel_341, retro_tbel_3431, retro_tbel_3444, retro_tbel_3555, retro_tbel_3640, retro_tbel_3695, retro_tbel_3915, retro_tbel_3975, retro_tbel_4026, retro_tbel_4219, retro_tbel_4252, retro_tbel_4259, retro_tbel_4355, retro_tbel_4423, retro_tbel_4479, retro_tbel_496, retro_tbel_565, retro_tbel_645, retro_tbel_666, retro_tbel_782, retro_tbel_802, retro_tbel_916,
Tursiops truncatus	ENSTTRG00000014496	24 retrocopies	retro_ttru_1160, retro_ttru_1216, retro_ttru_1222, retro_ttru_1287, retro_ttru_1326, retro_ttru_1432, retro_ttru_1463, retro_ttru_148, retro_ttru_1572, retro_ttru_1693, retro_ttru_1705, retro_ttru_176, retro_ttru_1835, retro_ttru_190, retro_ttru_194, retro_ttru_303, retro_ttru_331, retro_ttru_404, retro_ttru_427, retro_ttru_477, retro_ttru_576, retro_ttru_693, retro_ttru_879, retro_ttru_967,
Vicugna pacos	ENSVPAG00000012307	4 retrocopies	retro_vpac_22, retro_vpac_293, retro_vpac_440, retro_vpac_553,