RetrogeneDB ID: retro_eeur_77

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_458:14053..14428(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM230
• Ensembl ID: ENSEEUG00000014992
• Aliases: None
• Description: transmembrane protein 230 [Source:HGNC Symbol;Acc:15876]

Sequence

>retro_eeur_77
CTGTGTCACTGTTTTATGATGCCATCCCATACCAACCTGGCTATTGGAATCTCTAATAGTAAAATGAAATACTCAAGGCT
CACCAGCACAGACGACGGCTACATTGACCTTCAGTTTAAGAAAAGCCCTCCTAAGATTCCATATAAGGCCACTGCGCTTG
CTACAGTGCTGTTTTTGATTGGTGCCTTTCTCATTATCGTAGGCTCCCTCCTCCTAGCTGGATAGATCAGCAAAGGGGGA
GCAGACTGAGCTGTTCCTGTCCTGATTATTGGCATACTGGTGTTCCTACCAGGATTTTACCACCTGTGCATCACTTACTA
TGCATCCAAAGGCTACTGGGATTACTCCTATGATGGTATTCCAGACTTTGATGAT

Alignment

ORF - retro_eeur_77 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LCHCVMMPSRTNLATGIPNSKVKYSRLASTDDGYIDLQFKKSPPKIPYKAIALATVLFLIGAFLIIIGSL
          LCHC.MMPS.TNLA.GI.NSK.KYSRL.STDDGYIDLQFKKSPPKIPYKA.ALATVLFLIGAFLII.GSL
Retrocopy LCHCFMMPSHTNLAIGISNSKMKYSRLTSTDDGYIDLQFKKSPPKIPYKATALATVLFLIGAFLIIVGSL

Parental  LLAGYISKGGADRAVPVLIIGILVFLPGFYHLRIAYYASKGYRGYSYDDIPDFDD
          LLAG.ISKGGAD.AVPVLIIGILVFLPGFYHL.I.YYASKGY..YSYD.IPDFDD
Retrocopy LLAG*ISKGGAD*AVPVLIIGILVFLPGFYHLCITYYASKGYWDYSYDGIPDFDD

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	0.32 RPM	8.70 RPM
SRP017611_kidney	0.38 RPM	39.20 RPM
SRP017611_liver	0.00 RPM	20.26 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_77 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 40 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006063	2 retrocopies	retro_btau_1079, retro_btau_147,
Choloepus hoffmanni	ENSCHOG00000010231	12 retrocopies	retro_chof_1228, retro_chof_1463, retro_chof_1812, retro_chof_2199, retro_chof_2210, retro_chof_2400, retro_chof_253, retro_chof_2584, retro_chof_2661, retro_chof_397, retro_chof_884, retro_chof_996,
Callithrix jacchus	ENSCJAG00000021275	2 retrocopies	retro_cjac_3112, retro_cjac_4206,
Erinaceus europaeus	ENSEEUG00000014992	1 retrocopy	retro_eeur_77 ,
Homo sapiens	ENSG00000089063	3 retrocopies	retro_hsap_4890, retro_hsap_550, retro_hsap_783,
Loxodonta africana	ENSLAFG00000006412	1 retrocopy	retro_lafr_1033,
Myotis lucifugus	ENSMLUG00000023089	2 retrocopies	retro_mluc_1504, retro_mluc_1759,
Macaca mulatta	ENSMMUG00000013258	4 retrocopies	retro_mmul_1187, retro_mmul_2386, retro_mmul_2626, retro_mmul_856,
Nomascus leucogenys	ENSNLEG00000007719	3 retrocopies	retro_nleu_1256, retro_nleu_199, retro_nleu_723,
Otolemur garnettii	ENSOGAG00000001386	2 retrocopies	retro_ogar_1700, retro_ogar_3108,
Pongo abelii	ENSPPYG00000010796	3 retrocopies	retro_pabe_3801, retro_pabe_507, retro_pabe_916,
Pan troglodytes	ENSPTRG00000013221	4 retrocopies	retro_ptro_3030, retro_ptro_3257, retro_ptro_3258, retro_ptro_413,
Ictidomys tridecemlineatus	ENSSTOG00000019378	1 retrocopy	retro_itri_35,