RetrogeneDB ID: retro_eeur_284

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_239754:1..275(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB11B
• Ensembl ID: ENSEEUG00000009165
• Aliases: None
• Description: RAB11B, member RAS oncogene family [Source:HGNC Symbol;Acc:9761]

Sequence

>retro_eeur_284
ATGGGGAACGGGGACGATGAGTACCACTACCTATTCAAAGTGGTGCTGATCGGGAACTCAGGCGTGGGCAAGAGCAACCT
CCTGTCCCGCTTCACCCGCAACGGGTTCAACTTAGAAAGCAAGAGCACCATCGGCGTGGAGTTCGCCACCCGCAGCATCC
AGGTGGACGGCAAGACCATCCAGGCGCAGATATGGGACACAGCCCGCCAGGAGCGCTACCGGGCCGTCACACTCGGCGTA
CTACCCCGGGGCGGTGGGCGCGCTGCTGGTCTAC

Alignment

ORF - retro_eeur_284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.13 %
• Parental protein coverage: 63.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGTRDDEYDYLFKVVLIGDSGVGKSNLLSRFTRNEFNLESKSTIGVEFATRSIQVDGKTIKAQIWDTAGQ
          MG..DDEY.YLFKVVLIG.SGVGKSNLLSRFTRN.FNLESKSTIGVEFATRSIQVDGKTI.AQIWDTA.Q
Retrocopy MGNGDDEYHYLFKVVLIGNSGVGKSNLLSRFTRNGFNLESKSTIGVEFATRSIQVDGKTIQAQIWDTARQ

Parental  ERYRAIT-SAYYRGAVGALLVY
          ERYRA.T.SAYY.GAVGALLVY
Retrocopy ERYRAVT>SAYYPGAVGALLVY

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	4.83 RPM	3.06 RPM
SRP017611_kidney	5.06 RPM	8.81 RPM
SRP017611_liver	1.45 RPM	1.13 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_284 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 9 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013525	1 retrocopy	retro_chof_1582,
Callithrix jacchus	ENSCJAG00000010778	2 retrocopies	retro_cjac_3866, retro_cjac_3917,
Erinaceus europaeus	ENSEEUG00000007700	1 retrocopy	retro_eeur_496,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284 , retro_eeur_565,
Mus musculus	ENSMUSG00000077450	1 retrocopy	retro_mmus_1846,
Otolemur garnettii	ENSOGAG00000003227	1 retrocopy	retro_ogar_2405,
Petromyzon marinus	ENSPMAG00000009335	1 retrocopy	retro_pmar_25,
Pteropus vampyrus	ENSPVAG00000009645	1 retrocopy	retro_pvam_64,
Tupaia belangeri	ENSTBEG00000000667	1 retrocopy	retro_tbel_4634,