RetrogeneDB ID: retro_eeur_496

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_327240:4384..4786(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB2A
• Ensembl ID: ENSEEUG00000007700
• Aliases: None
• Description: RAB2A, member RAS oncogene family [Source:HGNC Symbol;Acc:9763]

Sequence

>retro_eeur_496
GTAGAGTTCGGTGCTCGAATGATAACTATTGATGGCAAACAAATTAAACTTCAGATATGGGACACGGCAGGACAGGAGTC
CTTTCGTTCCATCACCAGGTCATATTACAGGGGCGCAGCGGGAGCTTTGCTAGTGTATGATATTACAAGGAGAGATACAT
TCAACCACTTGACAACCTGGTTGGAAGATGCCCGCCAACATTTCAATTCCAACATGGTCATGCTTATCGGGAATAAAAGT
GATTTAGAATCTAGAAGAGAGGTAAAAAAAGAAGAAGGTGAAGCCTTTGTACGAGAACATGGTCTCATCTTCATGGAAAC
TTCTGCCAAGACTGCTTCCAATGTAGAAGAGGCATTTATTAACACAGCAAAAGAAATTTATGAAAAAAAGAAGGAGTCTT
TG

Alignment

ORF - retro_eeur_496 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.81 %
• Parental protein coverage: 75.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQHSNS
          VEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQH.NS
Retrocopy VEFGARMITIDGKQIKLQIWDTAGQESFRSITRSYYRGAAGALLVYDITRRDTFNHLTTWLEDARQHFNS

Parental  NMVIMLIGNKSDLESRREVKKEEGEAFAREHGLIFMETSAKTASNVEEAFINTAKEIYEKIQEGV
          NMV.MLIGNKSDLESRREVKKEEGEAF.REHGLIFMETSAKTASNVEEAFINTAKEIYEK..E..
Retrocopy NMV-MLIGNKSDLESRREVKKEEGEAFVREHGLIFMETSAKTASNVEEAFINTAKEIYEKKKESL

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	41.90 RPM	57.21 RPM
SRP017611_kidney	31.32 RPM	37.51 RPM
SRP017611_liver	14.31 RPM	13.67 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_496 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007700	1 retrocopy	retro_eeur_496 ,
Erinaceus europaeus	ENSEEUG00000009165	2 retrocopies	retro_eeur_284, retro_eeur_565,
Echinops telfairi	ENSETEG00000010340	2 retrocopies	retro_etel_203, retro_etel_32,
Monodelphis domestica	ENSMODG00000008556	2 retrocopies	retro_mdom_1999, retro_mdom_989,
Mus musculus	ENSMUSG00000047187	1 retrocopy	retro_mmus_2650,