RetrogeneDB ID: retro_eeur_556

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_343925:3555..3876(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TCEB1
• Ensembl ID: ENSEEUG00000005157
• Aliases: None
• Description: transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C) [Source:HGNC Symbol;Acc:11617]

Sequence

>retro_eeur_556
GAGAAGACCTACGGTGGCTGTGAAGGCCCTGAAGCCATGTATGTCAAACTGATATCATCGGATGGCCATGAATTTATCAT
GATAAAGAGAACATGCATTGACATCAGGACCGATAAAAGCCATGGTAGGTGGCCCAGGTCAGTTTGCTGAAAATGAAACC
AATGAAATCAATTTTAGGGAGATCCCTTCACATGTGCTATCAAAAGTAAGTATGTATTTTACCTACAAGGTTAGCTACAC
TAACAGTTCTACCAAGATTCCTCAATTCCCAATTGCACTGGAAATTCATTGGAACTGCTTATGGCTGTGAACTTCCTAGA
T

Alignment

ORF - retro_eeur_556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 98.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DKTYGGCEGPDAMYVKLISSNGHEFIVK-REHALTSGTITAMLSGPXQFAENETNEVNFREIPSHVLSKV
          .KTYGGCEGP.AMYVKLISS.GHEFI...REHALTSG.I.AM..GP.QFAENETNE.NFREIPSHVLSKV
Retrocopy EKTYGGCEGPEAMYVKLISSDGHEFIMI>REHALTSGPIKAMVGGPGQFAENETNEINFREIPSHVLSKV

Parental  CMYFTYKVRYTNSSTEIPEFPIAPEI-ALELLMAANFLD
          .MYFTYKV.YTNSST.IP.FPIA.EI..LELLMA.NFLD
Retrocopy SMYFTYKVSYTNSSTKIPQFPIALEI<SLELLMAVNFLD

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	2.42 RPM
SRP017611_kidney	0.00 RPM	2.06 RPM
SRP017611_liver	0.00 RPM	1.61 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_556 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 2 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000005157	3 retrocopies	retro_eeur_181, retro_eeur_271, retro_eeur_556 ,
Macropus eugenii	ENSMEUG00000015988	11 retrocopies	retro_meug_1209, retro_meug_1508, retro_meug_1531, retro_meug_1642, retro_meug_1740, retro_meug_1764, retro_meug_308, retro_meug_398, retro_meug_743, retro_meug_768, retro_meug_815,