RetrogeneDB ID: retro_eeur_400

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_284885:4002..4414(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000014996
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL15
• Ensembl ID: ENSEEUG00000011286
• Aliases: None
• Description: ribosomal protein L15 [Source:HGNC Symbol;Acc:10306]

Sequence

>retro_eeur_400
GACAAAGCCCAAAGGCTGGGCTACAAGGCCTAGCAAGGTTACGTCATATATCAGATTCGTGTCCGCTGTGGTGGCCACAA
ACATCCAGTTCCCAAGGGTGCAACCTATGGTAAGCCCACCCATCATGGAGTCAACCAGCTGAAGTTTGCACAGAGCCTTT
AGTCTGTTGCTGAGGAGCGAACTGGACACCACTGTGGGGCTCTGAGAGTCCTGAATTCTTACTGGGTGGGTGAAGATTCC
ACATACAAGTTCTTTGAGGTTATCCTTATTGATCCATTCCATAAAGCTATCAGAAGAAATCCTGACACCCAATGGATCAC
CAAACCAGTCCATAGCACAGGGAGATGCGGGGGTGACATCCGCAGGACACAAGAGCCACGGCCTTGGAAAGGGCCACAAG
TTCCACCACACC

Alignment

ORF - retro_eeur_400 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.86 %
• Parental protein coverage: 65.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKARRLGYKAKQGYVIYRIRVRRGGRKRPVPKGATYGKPVHHGVNQLKFARSLQSVAEERAGRHCGALRV
          DKA.RLGYKA.QGYVIY.IRVR.GG.K.PVPKGATYGKP.HHGVNQLKFA.SL.SVAEER.G.HCGALRV
Retrocopy DKAQRLGYKA*QGYVIYQIRVRCGGHKHPVPKGATYGKPTHHGVNQLKFAQSL*SVAEERTGHHCGALRV

Parental  LNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHK-HREMR-GLTSAGRKSRGLGKGHKFHHT
          LNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVH..HREMR.G.TSAG.KS.GLGKGHKFHHT
Retrocopy LNSYWVGEDSTYKFFEVILIDPFHKAIRRNPDTQWITKPVHS<HREMR<GVTSAGHKSHGLGKGHKFHHT

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	48.99 RPM
SRP017611_kidney	0.38 RPM	131.28 RPM
SRP017611_liver	0.00 RPM	73.31 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_400 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 13 parental genes, and 99 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000033080	2 retrocopies	retro_btau_152, retro_btau_201,
Erinaceus europaeus	ENSEEUG00000011286	5 retrocopies	retro_eeur_200, retro_eeur_28, retro_eeur_400 , retro_eeur_685, retro_eeur_694,
Echinops telfairi	ENSETEG00000015044	4 retrocopies	retro_etel_1438, retro_etel_431, retro_etel_658, retro_etel_943,
Macropus eugenii	ENSMEUG00000014522	3 retrocopies	retro_meug_1678, retro_meug_2006, retro_meug_2112,
Macaca mulatta	ENSMMUG00000006353	1 retrocopy	retro_mmul_209,
Mustela putorius furo	ENSMPUG00000012148	7 retrocopies	retro_mputfur_1011, retro_mputfur_1252, retro_mputfur_1291, retro_mputfur_314, retro_mputfur_346, retro_mputfur_658, retro_mputfur_669,
Mus musculus	ENSMUSG00000012405	2 retrocopies	retro_mmus_118, retro_mmus_8,
Otolemur garnettii	ENSOGAG00000013056	13 retrocopies	retro_ogar_1066, retro_ogar_1129, retro_ogar_1182, retro_ogar_1453, retro_ogar_1483, retro_ogar_1629, retro_ogar_1809, retro_ogar_2378, retro_ogar_270, retro_ogar_3058, retro_ogar_3096, retro_ogar_3349, retro_ogar_903,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Rattus norvegicus	ENSRNOG00000008140	17 retrocopies	retro_rnor_1046, retro_rnor_1409, retro_rnor_1497, retro_rnor_1685, retro_rnor_1690, retro_rnor_1785, retro_rnor_2042, retro_rnor_2249, retro_rnor_2313, retro_rnor_2451, retro_rnor_2473, retro_rnor_2786, retro_rnor_2997, retro_rnor_428, retro_rnor_66, retro_rnor_710, retro_rnor_844,
Sus scrofa	ENSSSCG00000028079	5 retrocopies	retro_sscr_1219, retro_sscr_1225, retro_sscr_448, retro_sscr_968, retro_sscr_997,
Tupaia belangeri	ENSTBEG00000009843	34 retrocopies	retro_tbel_1031, retro_tbel_1072, retro_tbel_1322, retro_tbel_1346, retro_tbel_1363, retro_tbel_1524, retro_tbel_1668, retro_tbel_1931, retro_tbel_1980, retro_tbel_2035, retro_tbel_2212, retro_tbel_2270, retro_tbel_2453, retro_tbel_2634, retro_tbel_2818, retro_tbel_3196, retro_tbel_3208, retro_tbel_3387, retro_tbel_3449, retro_tbel_352, retro_tbel_3936, retro_tbel_4079, retro_tbel_4417, retro_tbel_4433, retro_tbel_4477, retro_tbel_4564, retro_tbel_4705, retro_tbel_476, retro_tbel_555, retro_tbel_727, retro_tbel_746, retro_tbel_84, retro_tbel_929, retro_tbel_992,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,