RetrogeneDB ID: retro_eeur_297

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_245798:6456..7215(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS3A
• Ensembl ID: ENSEEUG00000004994
• Aliases: None
• Description: ribosomal protein S3A [Source:HGNC Symbol;Acc:10421]

Sequence

>retro_eeur_297
GGCAAAAATGAGGGAGCCAAGAAGAAAGTGGTTGATCCATTTTCGAAGAAGGACTGGTACGATGTGAAAGCGCCAGCAAT
GTTCAACATAAGGAATATTGGGAAGACACTAGTCACAAGAACTCAAGGAACCAAGATCGCATCTGACGGCCTGAAGGGTC
ATGTGTTTGAAGTGAGCCTTGCTGATCTGCAGAATGATGAAGTTGCATTTAGAAAATTCAAACTCGTTACTGAGGATGTT
CAAGGCAGAAACTGCCCAACTAACTTTCATGGCATGGACCTCACCCGGGATTAAATGTGCTCCATGGTCAAAAAATGGCA
GACCATGATTGAAGCTCATGTTGATGTAAAGACTACCGATGGCTATTTGCTTTGTCTATTCTGTGTGGGGTTTACTAAAA
AACACAACAACCAGATTCAAAAGACCTCTTATGCTCAACACCAACAAGTTCGACAAATTTGGAAAAAGATGATGGAAATC
ATGACCCAAGAGGTGCAGACAAATGACTTAAAAGAGGTGGTCAACAAGTTGATTCCCGATAGCATTGGGAAAGACATAGA
AAAAGCTTGCCAGTCTATTTACCCACTTCATGATGTCTTTGTTAGAAAAGTGAAAATGCTGAAGAAGCCCAAGTTGGAAT
TGGGAAAACTCATGGAGCTTCATGGAGAAGGTGGTAGTTCTGGGAAAACTACTGGAGATGAGACTGGTGCTAAAGTTGAG
TTGGCCAATGGATATGAACCATCAGTCCAAGAATCTGTC

Alignment

ORF - retro_eeur_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.09 %
• Parental protein coverage: 95.83 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGKKGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGRVFEVSLADLQNDEVAF
          G...GAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKG.VFEVSLADLQNDEVAF
Retrocopy GKNEGAKKKVVDPFSKKDWYDVKAPAMFNIRNIGKTLVTRTQGTKIASDGLKGHVFEVSLADLQNDEVAF

Parental  RKFKLITEDDQGKNCLTNFHGMDLTRDKMCSMVKKQWTMIEAHVDVKTTDGYLLRLFCVGFTKKRNNQIR
          RKFKL.TED.QG.NC.TNFHGMDLTRD.MCSMVKK..TMIEAHVDVKTTDGYLL.LFCVGFTKK.NNQI.
Retrocopy RKFKLVTEDVQGRNCPTNFHGMDLTRD*MCSMVKKWQTMIEAHVDVKTTDGYLLCLFCVGFTKKHNNQIQ

Parental  KTSYAQHQQVRQIRKKMMEIMTREVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKP
          KTSYAQHQQVRQI.KKMMEIMT.EVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKP
Retrocopy KTSYAQHQQVRQIWKKMMEIMTQEVQTNDLKEVVNKLIPDSIGKDIEKACQSIYPLHDVFVRKVKMLKKP

Parental  KFELGKLMELHGEGGSSGKTTGDETGAKVERADGYEPPVQESV
          K.ELGKLMELHGEGGSSGKTTGDETGAKVE.A.GYEP.VQESV
Retrocopy KLELGKLMELHGEGGSSGKTTGDETGAKVELANGYEPSVQESV

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	0.00 RPM	171.46 RPM
SRP017611_kidney	0.00 RPM	311.88 RPM
SRP017611_liver	0.00 RPM	246.47 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_297 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 21 parental genes, and 187 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009908	3 retrocopies	retro_btau_1284, retro_btau_1733, retro_btau_233,
Canis familiaris	ENSCAFG00000007990	7 retrocopies	retro_cfam_103, retro_cfam_146, retro_cfam_169, retro_cfam_170, retro_cfam_179, retro_cfam_222, retro_cfam_77,
Callithrix jacchus	ENSCJAG00000002268	7 retrocopies	retro_cjac_2, retro_cjac_21, retro_cjac_249, retro_cjac_312, retro_cjac_337, retro_cjac_368, retro_cjac_78,
Cavia porcellus	ENSCPOG00000015569	9 retrocopies	retro_cpor_1154, retro_cpor_1229, retro_cpor_210, retro_cpor_383, retro_cpor_460, retro_cpor_555, retro_cpor_609, retro_cpor_646, retro_cpor_789,
Dipodomys ordii	ENSDORG00000002250	10 retrocopies	retro_dord_142, retro_dord_168, retro_dord_193, retro_dord_209, retro_dord_229, retro_dord_314, retro_dord_380, retro_dord_752, retro_dord_757, retro_dord_95,
Equus caballus	ENSECAG00000009573	6 retrocopies	retro_ecab_168, retro_ecab_222, retro_ecab_256, retro_ecab_597, retro_ecab_626, retro_ecab_885,
Erinaceus europaeus	ENSEEUG00000004994	4 retrocopies	retro_eeur_297 , retro_eeur_510, retro_eeur_517, retro_eeur_66,
Felis catus	ENSFCAG00000031288	5 retrocopies	retro_fcat_1110, retro_fcat_134, retro_fcat_1878, retro_fcat_780, retro_fcat_858,
Gorilla gorilla	ENSGGOG00000003182	2 retrocopies	retro_ggor_70, retro_ggor_97,
Loxodonta africana	ENSLAFG00000017660	3 retrocopies	retro_lafr_10, retro_lafr_38, retro_lafr_385,
Myotis lucifugus	ENSMLUG00000014788	8 retrocopies	retro_mluc_1197, retro_mluc_1397, retro_mluc_1568, retro_mluc_1846, retro_mluc_2130, retro_mluc_2158, retro_mluc_2388, retro_mluc_862,
Macaca mulatta	ENSMMUG00000021821	1 retrocopy	retro_mmul_2297,
Monodelphis domestica	ENSMODG00000000969	6 retrocopies	retro_mdom_1040, retro_mdom_1229, retro_mdom_1396, retro_mdom_1480, retro_mdom_627, retro_mdom_694,
Mustela putorius furo	ENSMPUG00000007139	8 retrocopies	retro_mputfur_1293, retro_mputfur_1363, retro_mputfur_278, retro_mputfur_316, retro_mputfur_504, retro_mputfur_695, retro_mputfur_764, retro_mputfur_847,
Mus musculus	ENSMUSG00000028081	2 retrocopies	retro_mmus_218, retro_mmus_254,
Oryctolagus cuniculus	ENSOCUG00000007011	1 retrocopy	retro_ocun_257,
Rattus norvegicus	ENSRNOG00000011893	1 retrocopy	retro_rnor_198,
Sarcophilus harrisii	ENSSHAG00000015088	2 retrocopies	retro_shar_777, retro_shar_95,
Sus scrofa	ENSSSCG00000009019	3 retrocopies	retro_sscr_27, retro_sscr_749, retro_sscr_762,
Ictidomys tridecemlineatus	ENSSTOG00000024203	1 retrocopy	retro_itri_58,
Tupaia belangeri	ENSTBEG00000002963	98 retrocopies	retro_tbel_1005, retro_tbel_11, retro_tbel_1119, retro_tbel_116, retro_tbel_1232, retro_tbel_1318, retro_tbel_133, retro_tbel_137, retro_tbel_1375, retro_tbel_1378, retro_tbel_1383, retro_tbel_1417, retro_tbel_1421, retro_tbel_1509, retro_tbel_1686, retro_tbel_1698, retro_tbel_172, retro_tbel_1720, retro_tbel_1721, retro_tbel_1744, retro_tbel_1814, retro_tbel_1829, retro_tbel_1856, retro_tbel_1896, retro_tbel_1948, retro_tbel_1960, retro_tbel_1999, retro_tbel_206, retro_tbel_2200, retro_tbel_2306, retro_tbel_2463, retro_tbel_2483, retro_tbel_2510, retro_tbel_2626, retro_tbel_2654, retro_tbel_2657, retro_tbel_2745, retro_tbel_2759, retro_tbel_2760, retro_tbel_2764, retro_tbel_281, retro_tbel_2857, retro_tbel_2957, retro_tbel_2959, retro_tbel_3114, retro_tbel_317, retro_tbel_3212, retro_tbel_3255, retro_tbel_3259, retro_tbel_3299, retro_tbel_336, retro_tbel_3372, retro_tbel_3416, retro_tbel_3471, retro_tbel_3486, retro_tbel_3513, retro_tbel_3558, retro_tbel_3613, retro_tbel_3631, retro_tbel_3655, retro_tbel_3705, retro_tbel_373, retro_tbel_375, retro_tbel_3755, retro_tbel_3786, retro_tbel_3815, retro_tbel_3823, retro_tbel_3832, retro_tbel_386, retro_tbel_3882, retro_tbel_39, retro_tbel_3947, retro_tbel_3966, retro_tbel_399, retro_tbel_4116, retro_tbel_4144, retro_tbel_4147, retro_tbel_4211, retro_tbel_4220, retro_tbel_423, retro_tbel_4294, retro_tbel_4304, retro_tbel_4347, retro_tbel_438, retro_tbel_4428, retro_tbel_445, retro_tbel_4579, retro_tbel_598, retro_tbel_619, retro_tbel_623, retro_tbel_671, retro_tbel_859, retro_tbel_90, retro_tbel_912, retro_tbel_92, retro_tbel_928, retro_tbel_956, retro_tbel_973,