RetrogeneDB ID: retro_eeur_198

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_206553:4504..4983(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IDI1
• Ensembl ID: ENSEEUG00000012555
• Aliases: None
• Description: isopentenyl-diphosphate delta isomerase 1 [Source:HGNC Symbol;Acc:5387]

Sequence

>retro_eeur_198
AAGCTCTTGTTACAACAGAGATCAGACACTAAAATTACCTTTCCAGGTTGTTTTACCAGTACTTGTTGTAGTCACCCACT
AAGTAATCCAGGAGAGCTTGAAGAAAGTGATGCGATTGGAGTGAAAAGAGCAGTTCAGAGGCGTTTGAAAGTTGATTTAT
GCATTCCCCTGGAAGAGGTTCCTCCAGAAGAAATTAAGTACCTAACACGAATGTAGTACAAGGCTCAATCTGATAGCATT
TGGGGAGAACATGAGATTGATTACATTTTGTTTATGAAGAAGAATCCAGATTCCAATGAGATTAAAAGCTATTGTATGTG
TCAAAGGAAGAAGTAAAAGAACTTTTGAGAAAGGCAGCCACTGGTGAAATTAAGTTAACTCCATGGTTTAAGATTATTAC
AGAGGCTTTTCTCTTTAAATGGTGGGACAGTTTACATAATCTGAATGTGTTTATTGACCATGAGAAAATACACAGAATG

Alignment

ORF - retro_eeur_198 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.06 %
• Parental protein coverage: 69.2 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KLLLQQRSDAKITFPGCFTNTCCSHPLNNPGELEENDAIGVRRAAQRRLKAELGIPLEEVPPEEIQYLTR
          KLLLQQRSD.KITFPGCFT.TCCSHPL.NPGELEE.DAIGV.RA.QRRLK..L.IPLEEVPPEEI.YLTR
Retrocopy KLLLQQRSDTKITFPGCFTSTCCSHPLSNPGELEESDAIGVKRAVQRRLKVDLCIPLEEVPPEEIKYLTR

Parental  LYYKAQSDDIWGEHEIDYILFMKKNVTLNPDPNEIKSYC-YVSKEEVKELLRKAATGKIKLTPWFKIITE
          ..YKAQSD.IWGEHEIDYILFMKKN....PD.NEIKSYC.YVSKEEVKELLRKAATG.IKLTPWFKIITE
Retrocopy M*YKAQSDSIWGEHEIDYILFMKKN----PDSNEIKSYC<YVSKEEVKELLRKAATGEIKLTPWFKIITE

Parental  TFLFKWWDNLHNLDVFIDHEKIHRM
          .FLFKWWD.LHNL.VFIDHEKIHRM
Retrocopy AFLFKWWDSLHNLNVFIDHEKIHRM

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	0.16 RPM	25.14 RPM
SRP017611_kidney	0.00 RPM	12.19 RPM
SRP017611_liver	0.48 RPM	27.33 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_198 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 14 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008483	3 retrocopies	retro_cjac_2083, retro_cjac_2591, retro_cjac_2820,
Erinaceus europaeus	ENSEEUG00000012555	3 retrocopies	retro_eeur_188, retro_eeur_198 , retro_eeur_61,
Homo sapiens	ENSG00000067064	3 retrocopies	retro_hsap_2161, retro_hsap_2444, retro_hsap_4053,
Gorilla gorilla	ENSGGOG00000000934	3 retrocopies	retro_ggor_1521, retro_ggor_1717, retro_ggor_2722,
Macaca mulatta	ENSMMUG00000017115	3 retrocopies	retro_mmul_2340, retro_mmul_632, retro_mmul_899,
Monodelphis domestica	ENSMODG00000005998	5 retrocopies	retro_mdom_1107, retro_mdom_1692, retro_mdom_1697, retro_mdom_1724, retro_mdom_547,
Mus musculus	ENSMUSG00000058258	4 retrocopies	retro_mmus_2032, retro_mmus_2660, retro_mmus_417, retro_mmus_552,
Nomascus leucogenys	ENSNLEG00000013594	3 retrocopies	retro_nleu_1810, retro_nleu_2777, retro_nleu_2804,
Oryctolagus cuniculus	ENSOCUG00000007493	1 retrocopy	retro_ocun_267,
Ochotona princeps	ENSOPRG00000008692	2 retrocopies	retro_opri_694, retro_opri_755,
Pongo abelii	ENSPPYG00000002039	2 retrocopies	retro_pabe_1783, retro_pabe_3327,
Pan troglodytes	ENSPTRG00000002239	3 retrocopies	retro_ptro_1412, retro_ptro_1647, retro_ptro_2747,
Ictidomys tridecemlineatus	ENSSTOG00000023260	1 retrocopy	retro_itri_118,
Tursiops truncatus	ENSTTRG00000011174	1 retrocopy	retro_ttru_255,