RetrogeneDB ID: retro_eeur_362

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_269774:6173..6614(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000006901
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MEAF6
• Ensembl ID: ENSEEUG00000013971
• Aliases: None
• Description: MYST/Esa1-associated factor 6 [Source:HGNC Symbol;Acc:25674]

Sequence

>retro_eeur_362
GAAGCACTGGCCAAATTGGAGAGACAGGTCTATGCTTTTGAAGGAAGCTATCTGGAAGACACTCAGATGTATGGCAATAT
TATCCGAGGCTGGGACCGGTATCTGACCAACCAAAAAAACTCCAATAGCACAAACGATCGAAGGAACCGGAAATTTAAGG
AAGCTGAGCGCCTCTTCAGTAAATCCTCAGTTACTTCAGCAGCTGCAGTAAGTGCATTGGCGGGAGTTCAGGACCAGCTC
ATTGAAAAAAAGAGAGCCAGGAAGTGGGACAGAAAGTGATACTTCTCCAGACTTCCACAATCAGGAAAATGAGGCCAGCC
AAGAGGACCCTGAGGATCTGGATGGATCTGTGCAAGGAGTGAAACCTCAGAAGGCTGCTTCTTCTACTTCCTCAGGGAGT
CATCACAGCAGCCATAAAAAACGAAAGAATAAAACCGACAC

Alignment

ORF - retro_eeur_362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.62 %
• Parental protein coverage: 85.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETLANLERQIYAFEGSYLEDTQMYGNIIRGWDRYLTNQKNSNSKNDRRNRKFKEAERLFSKSSVTSAAAV
          E.LA.LERQ.YAFEGSYLEDTQMYGNIIRGWDRYLTNQKNSNS.NDRRNRKFKEAERLFSKSSVTSAAAV
Retrocopy EALAKLERQVYAFEGSYLEDTQMYGNIIRGWDRYLTNQKNSNSTNDRRNRKFKEAERLFSKSSVTSAAAV

Parental  SALAGVQDQL-XXXXEPGSGTESDTSPDFHNQENEPSQEDPEDLDGSVQGVKPQKAASSTSSGSHHSSHK
          SALAGVQDQL.....EPGSGTESDTSPDFHNQENE.SQEDPEDLDGSVQGVKPQKAASSTSSGSHHSSHK
Retrocopy SALAGVQDQL>LKKREPGSGTESDTSPDFHNQENEASQEDPEDLDGSVQGVKPQKAASSTSSGSHHSSHK

Parental  KRKNK-NRH
          KRKNK.NRH
Retrocopy KRKNK<NRH

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	2.09 RPM	13.70 RPM
SRP017611_kidney	1.13 RPM	2.81 RPM
SRP017611_liver	0.00 RPM	0.16 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_362 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001927	1 retrocopy	retro_cjac_2767,
Cavia porcellus	ENSCPOG00000025988	1 retrocopy	retro_cpor_1252,
Erinaceus europaeus	ENSEEUG00000013971	3 retrocopies	retro_eeur_362 , retro_eeur_469, retro_eeur_654,
Macropus eugenii	ENSMEUG00000003403	3 retrocopies	retro_meug_1279, retro_meug_584, retro_meug_727,
Myotis lucifugus	ENSMLUG00000017128	2 retrocopies	retro_mluc_436, retro_mluc_960,
Otolemur garnettii	ENSOGAG00000006773	1 retrocopy	retro_ogar_2339,
Vicugna pacos	ENSVPAG00000001916	1 retrocopy	retro_vpac_566,