RetrogeneDB ID: retro_eeur_116

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7241:23053..23358(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ERH
• Ensembl ID: ENSEEUG00000007758
• Aliases: None
• Description: enhancer of rudimentary homolog (Drosophila) [Source:HGNC Symbol;Acc:3447]

Sequence

>retro_eeur_116
CACACCATTTTGTTGGTACAGCCTACCAAGAGGCCAGAAGGCAGAATTTATGCAGACTATGAATCTGTGAATGAATGCAC
GGAAAGTGTTTGTAAAATGTATAAAAAAGCATCTGAAAAGAATGAATCCCAACAGTCCCTCTATCACATGATATCAGTCA
GTTGTTTGATTTTATTGATGATCTGGCAGACTTCAGCTGTCTTATTTACTGAGCTGATACCCAGACACACCAACCTTATA
ACAAAGACTGGATTAAAGAGAAGATCTATATGCTTCTTCGTCAACAAGCCCAACAGGCTGAGAAA

Alignment

ORF - retro_eeur_116 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.77 %
• Parental protein coverage: 98.08 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  HTILLVQPTKRPEGRTYADYESVNECMEGVCKMYEE-HLKRMN-PNSPSITYDISQLFDFIDDLADLSCL
          HTILLVQPTKRPEGR.YADYESVNEC.E.VCKMY...HLKRMN.P..P....DISQLFDFIDDLAD.SCL
Retrocopy HTILLVQPTKRPEGRIYADYESVNECTESVCKMYKK>HLKRMN>PTVP-LSHDISQLFDFIDDLADFSCL

Parental  VYRADTQTYQPYNKDWIKEKIYVLLRRQAQQAGK
          .Y.ADTQT.QPYNKDWIKEKIY.LLR.QAQQA.K
Retrocopy IY*ADTQTHQPYNKDWIKEKIYMLLRQQAQQAEK

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	0.48 RPM	29.81 RPM
SRP017611_kidney	0.19 RPM	29.26 RPM
SRP017611_liver	0.00 RPM	12.70 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_116 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 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017798	4 retrocopies	retro_btau_1260, retro_btau_438, retro_btau_651, retro_btau_795,
Callithrix jacchus	ENSCJAG00000014940	2 retrocopies	retro_cjac_209, retro_cjac_846,
Equus caballus	ENSECAG00000019178	1 retrocopy	retro_ecab_45,
Erinaceus europaeus	ENSEEUG00000007758	6 retrocopies	retro_eeur_105, retro_eeur_108, retro_eeur_115, retro_eeur_116 , retro_eeur_185, retro_eeur_546,
Echinops telfairi	ENSETEG00000016172	5 retrocopies	retro_etel_1122, retro_etel_1451, retro_etel_715, retro_etel_716, retro_etel_975,
Homo sapiens	ENSG00000100632	2 retrocopies	retro_hsap_3594, retro_hsap_3799,
Myotis lucifugus	ENSMLUG00000011879	1 retrocopy	retro_mluc_142,
Oryctolagus cuniculus	ENSOCUG00000004636	1 retrocopy	retro_ocun_42,
Ochotona princeps	ENSOPRG00000000086	2 retrocopies	retro_opri_1140, retro_opri_519,
Pongo abelii	ENSPPYG00000005939	2 retrocopies	retro_pabe_2954, retro_pabe_3104,
Sus scrofa	ENSSSCG00000002307	1 retrocopy	retro_sscr_748,
Tursiops truncatus	ENSTTRG00000013963	2 retrocopies	retro_ttru_1671, retro_ttru_614,
Vicugna pacos	ENSVPAG00000006444	1 retrocopy	retro_vpac_423,