RetrogeneDB ID: retro_eeur_173

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_141764:623..1088(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SET
• Ensembl ID: ENSEEUG00000006238
• Aliases: None
• Description: SET nuclear oncogene [Source:HGNC Symbol;Acc:10760]

Sequence

>retro_eeur_173
TCTACACTGCTTGGAGAAGAGGATGAAGAGGCACTGCATTACTTGACAAGAGTTGAAGTGACAGAATTTGAAGATAGTAA
ATCAGGTAACAGAATAGACTTTTATTTTGTTGAAAACCCTTACTTTGAAAATAAAGTTCTCTCCAAAGAATTTTATCTGA
ATGAGAGTGGTGATCCTTCTTTTGAAGGATCCACTGAAATCAAATGGTAATCTGGAAAGGATTTGATCAAATGTTCAAGT
CAAACCCAAAATCAAACCAACAGAAAGAGACAGCATGAGGAACCAGAGAGCTTCTTCACCTGGTTTACTGACCATTTTGG
TGCAGTCGCAGGTGAGTTAGGAGAGGTCATTAAAGATGGTATCTGGCTAAATACACTACAGTACTACTTGGTTCCTGATA
TGGATGAGGAATAAGGTGAGGGGGAAGATGATGATGATGAAGAGGAAGAAGGATTAGAAGATATG

Alignment

ORF - retro_eeur_173 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.44 %
• Parental protein coverage: 55.52 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SALLGEEDEEALHYLTRVEVTEFEDIKSGYRIDFYFDENPYFENKVLSKEFHLNESGDPSSK-STEIKWK
          S.LLGEEDEEALHYLTRVEVTEFED.KSG.RIDFYF.ENPYFENKVLSKEF.LNESGDPS...STEIKW.
Retrocopy STLLGEEDEEALHYLTRVEVTEFEDSKSGNRIDFYFVENPYFENKVLSKEFYLNESGDPSFEGSTEIKW*

Parental  SGKDLTKRSSQTQNKASRKRQHEEPESFFTWFTDHSDAGADELGEVIKDDIWPNPLQYYLVPDMDDEEGE
          SGKDL.K.SSQTQN...RKRQHEEPESFFTWFTDH..A.A.ELGEVIKD.IW.N.LQYYLVPDMD.E.GE
Retrocopy SGKDLIKCSSQTQNQTNRKRQHEEPESFFTWFTDHFGAVAGELGEVIKDGIWLNTLQYYLVPDMDEE*GE

Parental  GEEDDDDDEEEEGLEDI
          GE..DDDDEEEEGLED.
Retrocopy GE--DDDDEEEEGLEDM

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	82.51 RPM
SRP017611_kidney	0.00 RPM	73.89 RPM
SRP017611_liver	0.00 RPM	21.38 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_173 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 11 parental genes, and 111 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015686	7 retrocopies	retro_amel_1093, retro_amel_1201, retro_amel_1459, retro_amel_1675, retro_amel_530, retro_amel_631, retro_amel_634,
Bos taurus	ENSBTAG00000020959	8 retrocopies	retro_btau_1179, retro_btau_1490, retro_btau_1519, retro_btau_1556, retro_btau_464, retro_btau_469, retro_btau_749, retro_btau_955,
Erinaceus europaeus	ENSEEUG00000006238	11 retrocopies	retro_eeur_152, retro_eeur_166, retro_eeur_173 , retro_eeur_210, retro_eeur_260, retro_eeur_287, retro_eeur_452, retro_eeur_659, retro_eeur_696, retro_eeur_700, retro_eeur_701,
Felis catus	ENSFCAG00000005848	2 retrocopies	retro_fcat_130, retro_fcat_89,
Myotis lucifugus	ENSMLUG00000014291	13 retrocopies	retro_mluc_1026, retro_mluc_1120, retro_mluc_1673, retro_mluc_1977, retro_mluc_2098, retro_mluc_2188, retro_mluc_2361, retro_mluc_2412, retro_mluc_2584, retro_mluc_419, retro_mluc_524, retro_mluc_855, retro_mluc_881,
Macaca mulatta	ENSMMUG00000008532	11 retrocopies	retro_mmul_1133, retro_mmul_1261, retro_mmul_1534, retro_mmul_2096, retro_mmul_2175, retro_mmul_2241, retro_mmul_2262, retro_mmul_2614, retro_mmul_362, retro_mmul_419, retro_mmul_569,
Mustela putorius furo	ENSMPUG00000013069	10 retrocopies	retro_mputfur_1330, retro_mputfur_1556, retro_mputfur_1581, retro_mputfur_1605, retro_mputfur_221, retro_mputfur_274, retro_mputfur_286, retro_mputfur_723, retro_mputfur_785, retro_mputfur_799,
Mus musculus	ENSMUSG00000054766	17 retrocopies	retro_mmus_1366, retro_mmus_1435, retro_mmus_1671, retro_mmus_1743, retro_mmus_2329, retro_mmus_2448, retro_mmus_2484, retro_mmus_2664, retro_mmus_2665, retro_mmus_3015, retro_mmus_3290, retro_mmus_345, retro_mmus_3513, retro_mmus_517, retro_mmus_887, retro_mmus_929, retro_mmus_967,
Nomascus leucogenys	ENSNLEG00000017595	2 retrocopies	retro_nleu_108, retro_nleu_870,
Otolemur garnettii	ENSOGAG00000007635	13 retrocopies	retro_ogar_115, retro_ogar_1370, retro_ogar_3084, retro_ogar_3186, retro_ogar_3195, retro_ogar_3289, retro_ogar_447, retro_ogar_465, retro_ogar_543, retro_ogar_565, retro_ogar_806, retro_ogar_899, retro_ogar_934,
Pongo abelii	ENSPPYG00000019659	17 retrocopies	retro_pabe_1076, retro_pabe_1110, retro_pabe_1150, retro_pabe_1218, retro_pabe_1452, retro_pabe_1717, retro_pabe_1771, retro_pabe_2549, retro_pabe_2557, retro_pabe_2740, retro_pabe_299, retro_pabe_3667, retro_pabe_400, retro_pabe_414, retro_pabe_470, retro_pabe_720, retro_pabe_838,