RetrogeneDB ID: retro_eeur_414

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_292267:11123..11640(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E1B
• Ensembl ID: ENSEEUG00000005920
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 1B [Source:HGNC Symbol;Acc:33179]

Sequence

>retro_eeur_414
CCAACTCTCTGGGCTCTGTGGTTCTTCAAGAATGAGCGCAGCTGGACCTGGAGGGAGAACCTGCAGACGGTCACCAGGTT
TGACACGGTGGAGGATTTCTGGGCATTGTATAACAACATCAAGCTGCCCAGCAAGCTCTCCCCAGGCTGCGACTATGCTC
TGTTCCAGGATGGCATCGAACCCATGTGAGAAGACAGCAGCAATAAGCAGGATGGCCATGGTTGGTGAGCCTGGCCAAGC
AGCTGCGCCACTTGGATCTGGACCACCTGTGGTTGGACACGATGTTTTGTCTGATCAGAGAGAGCTTCGGGGAGTAAGGC
CCAGACGTGTGCGGGGCTGTTGTCAACATCTGCACCAAGGGAGACAAGATTGTGCTGTGGACACTGGAAGCTGACAGCCA
GTCCAGCGTGATGCACATCGGGCGAGTCTACAAAGAACACTTGGGTCTCTCATGAAGGCCACCACTGGGTACCAGGCTCA
CGCAGAACACAGCCAGCAGAGCAACTCGCTGGCTAGG

Alignment

ORF - retro_eeur_414 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.43 %
• Parental protein coverage: 89.64 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PNSWALWFFKNERSRAWRENLQMVTRFDTVEDFWALYNNIKLPSKLSPGCDYALFRDGIEPMWEDSSNKR
          P..WALWFFKNERS..WRENLQ.VTRFDTVEDFWALYNNIKLPSKLSPGCDYALF.DGIEPM.EDSSNK.
Retrocopy PTLWALWFFKNERSWTWRENLQTVTRFDTVEDFWALYNNIKLPSKLSPGCDYALFQDGIEPM*EDSSNKQ

Parental  GGR-WLVSLAKQLRHLDLDRLWLDTMLCLIGEGFGDYGPDVCGAVVNIRTKGDKIALWTREADSQASVMH
          .G..WLVSLAKQLRHLDLD.LWLDTM.CLI.E.FG..GPDVCGAVVNI.TKGDKI.LWT.EADSQ.SVMH
Retrocopy DGH<WLVSLAKQLRHLDLDHLWLDTMFCLIRESFGE*GPDVCGAVVNICTKGDKIVLWTLEADSQSSVMH

Parental  IGRVYKECLGLS-MKATIGYQAHADTATKSNSLAR
          IGRVYKE.LGLS.MKAT.GYQAHA.....SNSLAR
Retrocopy IGRVYKEHLGLS<MKATTGYQAHAEHSQQSNSLAR

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 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_414 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Erinaceus europaeus	ENSEEUG00000005920	1 retrocopy	retro_eeur_414 ,
Erinaceus europaeus	ENSEEUG00000015153	2 retrocopies	retro_eeur_57, retro_eeur_668,
Loxodonta africana	ENSLAFG00000027919	1 retrocopy	retro_lafr_866,
Monodelphis domestica	ENSMODG00000005097	3 retrocopies	retro_mdom_1779, retro_mdom_47, retro_mdom_710,
Mus musculus	ENSMUSG00000074895	1 retrocopy	retro_mmus_510,
Nomascus leucogenys	ENSNLEG00000012532	1 retrocopy	retro_nleu_84,
Ochotona princeps	ENSOPRG00000008875	2 retrocopies	retro_opri_1088, retro_opri_21,
Tupaia belangeri	ENSTBEG00000001631	2 retrocopies	retro_tbel_3164, retro_tbel_3690,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,