RetrogeneDB ID: retro_eeur_117

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7299:77646..78195(+)
• Located in intron of: ENSEEUG00000015972

Retrocopy information

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

Parental gene information

• Parental gene symbol: MED8
• Ensembl ID: ENSEEUG00000002286
• Aliases: None
• Description: mediator complex subunit 8 [Source:HGNC Symbol;Acc:19971]

Sequence

>retro_eeur_117
GATGAAGATCTCATGCGGCAAATGGAAGGACAAGTACCTGTTTTCAGCCATGAAGTAGTTCCTGATCATCTGAGAACCAA
GCCTGACCCTGAGGTTGAAGAGCAAGAAAAACAGTTGACAACGGATGCTGCCCGCATTGGTGCTGATGCAGCTCAGAAGC
AGATCCAGAGCTTGAATAAAATGTGCTCAAACCTTCTGGAGAAAATCAGCAAGGAGGAATGAGAATCAGAGAGTGGAGGT
CTCTGGCCAAACAAGCAGACCTTTAACCCTGCAGACACCAATGCCTTGGTGGCAGCTATTGCCTTTGGGAAAGGGCTGTC
TAACTGGAGACCTTCAGGTAGTAGTGGCCCAGGCCAGCCAGGCCAACCAGGAGCTGAGACAATTCTTGCAGGAGCCTCAG
CATTACAGCAGGTGCAGATGGCAGGAGCTCCAGGCCAGCAGCAGCCACTGCTCAGTGGGTTGCAAATGGCCCAAGCAGGT
CAACCAGGAAAAATGTCAAGTGGAATAAAAACCAACATCAAGTCTGCTTCCATGCATCCCTACCAGCGG

Alignment

ORF - retro_eeur_117 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.72 %
• Parental protein coverage: 62.46 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DEDLMRQTEGRVPVFSHEVVPDHLRTKPDPEVEEQEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKIS
          DEDLMRQ.EG.VPVFSHEVVPDHLRTKPDPEVEEQEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKIS
Retrocopy DEDLMRQMEGQVPVFSHEVVPDHLRTKPDPEVEEQEKQLTTDAARIGADAAQKQIQSLNKMCSNLLEKIS

Parental  KEERESESGGLWPNKQTFNPADTNALVAAIAFGKGLSNWRPSGSSGPGQPGQPGAGTILAGASALQQVQM
          KEE.ESESGGLWPNKQTFNPADTNALVAAIAFGKGLSNWRPSGSSGPGQPGQPGA.TILAGASALQQVQM
Retrocopy KEE*ESESGGLWPNKQTFNPADTNALVAAIAFGKGLSNWRPSGSSGPGQPGQPGAETILAGASALQQVQM

Parental  AGAPGQQQPLLSGVQMAQAGQPGKMPSGIKTNIKSASMHPYQR
          AGAPGQQQPLLSG.QMAQAGQPGKM.SGIKTNIKSASMHPYQR
Retrocopy AGAPGQQQPLLSGLQMAQAGQPGKMSSGIKTNIKSASMHPYQR

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	1.29 RPM	15.15 RPM
SRP017611_kidney	0.94 RPM	18.94 RPM
SRP017611_liver	0.16 RPM	12.54 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_117 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002286	1 retrocopy	retro_eeur_117 ,
Macropus eugenii	ENSMEUG00000013567	1 retrocopy	retro_meug_1813,
Monodelphis domestica	ENSMODG00000011310	1 retrocopy	retro_mdom_1131,
Oryctolagus cuniculus	ENSOCUG00000027895	2 retrocopies	retro_ocun_1088, retro_ocun_67,