RetrogeneDB ID: retro_eeur_57

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_3073:24837..25350(+)
• Located in intron of: ENSEEUG00000012827

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E2
• Ensembl ID: ENSEEUG00000015153
• Aliases: None
• Description: eukaryotic translation initiation factor 4E family member 2 [Source:HGNC Symbol;Acc:3293]

Sequence

>retro_eeur_57
AACAAGTTCGACGTATTAAAAGATGATGACAGTGGGGACCATGATCAGAATGAAGAAGACAGCACACAGAAGGAGAATGA
GAAGAGAAAAACAGAATGGGACAAGAGTCAGAGCAGTAGCAAGAGGAAGGCTATTGTCCCCGGACTGGCAGAGCACCCCC
TGCAGTACAATTACACTTTCTAGTACTCCAGGAGGACCCCTGGTCGCCCCACCAGCTCACAGAGCTATGAGCAGAATATC
AAACAGATTGGCATCTTTGCCTCTGTGGAGCAGTTCTGGAGGTTTTACAGCCACATGGTTTGTCTTGGAGACCTGATAGT
CCACAGCAACTTCCACTTCTTCAGAGAAGGAATCAAACCAATGTGGGAGGAGGATGCAAATAAAAATGGTGCCAAGTGGG
TTATTTGGCTGCAAAAGGGCTTGCCGTCCCACTGTTGGGACAATCTCATCTTGACCATGTTAGGGGAATAGTTTGTGGTC
GGGGAGGAGATCTGTAGGGCTGTGTGGTCTCTG

Alignment

ORF - retro_eeur_57 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.87 %
• Parental protein coverage: 67.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKFDALKDDDSGDHDQNEENSTQKDGEKEKTERDKSQSSSKRKAVVPGPAEHPLQYNYTFWYSRRTPGRP
          NKFD.LKDDDSGDHDQNEE.STQK..EK.KTE.DKSQSSSKRKA.VPG.AEHPLQYNYTF.YSRRTPGRP
Retrocopy NKFDVLKDDDSGDHDQNEEDSTQKENEKRKTEWDKSQSSSKRKAIVPGLAEHPLQYNYTF*YSRRTPGRP

Parental  TSSQSYEQNIKQIGTFASVEQFWRFYSHMVRPGDLTGHSDFHLFKEGIKPMWEDDANKNGGKWIIRLRKG
          TSSQSYEQNIKQIG.FASVEQFWRFYSHMV..GDL..HS.FH.F.EGIKPMWE.DANKNG.KW.I.L.KG
Retrocopy TSSQSYEQNIKQIGIFASVEQFWRFYSHMVCLGDLIVHSNFHFFREGIKPMWEEDANKNGAKWVIWLQKG

Parental  LASRCWENLILAMLGEQFMVGEEICGAVVSV
          L.S.CW.NLIL.MLGE.F.VGEEIC.AV.S.
Retrocopy LPSHCWDNLILTMLGE*FVVGEEICRAVWSL

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	18.37 RPM
SRP017611_kidney	0.00 RPM	32.82 RPM
SRP017611_liver	0.00 RPM	20.42 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_57 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016456	1 retrocopy	retro_amel_1304,
Canis familiaris	ENSCAFG00000011328	1 retrocopy	retro_cfam_183,
Erinaceus europaeus	ENSEEUG00000005920	1 retrocopy	retro_eeur_414,
Erinaceus europaeus	ENSEEUG00000015153	2 retrocopies	retro_eeur_57 , retro_eeur_668,
Microcebus murinus	ENSMICG00000015082	2 retrocopies	retro_mmur_806, retro_mmur_975,
Myotis lucifugus	ENSMLUG00000011269	1 retrocopy	retro_mluc_60,
Mustela putorius furo	ENSMPUG00000005206	2 retrocopies	retro_mputfur_110, retro_mputfur_1554,
Nomascus leucogenys	ENSNLEG00000014333	1 retrocopy	retro_nleu_1189,
Pan troglodytes	ENSPTRG00000013043	1 retrocopy	retro_ptro_1816,
Sarcophilus harrisii	ENSSHAG00000013108	1 retrocopy	retro_shar_101,