RetrogeneDB ID: retro_eeur_107

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_6597:27215..27480(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOPT1
• Ensembl ID: ENSEEUG00000011728
• Aliases: None
• Description: apoptogenic 1, mitochondrial [Source:HGNC Symbol;Acc:20492]

Sequence

>retro_eeur_107
CCAGTTCCTTTTTACATTCCTGACAATGAGTTGCCATTGCAATGAAAGCTAAAACAATCAAGATAAGAAACACAAGAATG
GAACCAAATGTTCTGGGAAAACCAAAATTTGACTTTTAGTAAGGAAAAAGAGGAATTTATTCACTTAGGGTTAAAAGCTG
AAGGATGAGAATGAGAGCTGAATCAGGCGAAAAAGCAACATTGTTGAAGAAATGGCTGGTTTTTACAAGGAATTTTTAAG
TAAAAATTTGCAGAAGCATATGTAT

Alignment

ORF - retro_eeur_107 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.35 %
• Parental protein coverage: 70.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PVPFYIPDNELPLQ-KLKQSR-ETQEWNQMFWENQNLTFSKEKEEFIHSRLKAKG-LGLRAESGQ-KATL
          PVPFYIPDNELPLQ.KLKQSR.ETQEWNQMFWENQNLTFSKEKEEFIH..LKA.G....RAESG..K...
Retrocopy PVPFYIPDNELPLQ*KLKQSR*ETQEWNQMFWENQNLTFSKEKEEFIHLGLKAEG<MRMRAESGE<KSNI

Parental  SADEMADFYKEFLSKNFQKHMY
          ...EMA.FYKEFLSKN.QKHMY
Retrocopy -VEEMAGFYKEFLSKNLQKHMY

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	8.54 RPM
SRP017611_kidney	0.00 RPM	9.00 RPM
SRP017611_liver	0.00 RPM	5.63 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_107 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030884	2 retrocopies	retro_cfam_1514, retro_cfam_396,
Dasypus novemcinctus	ENSDNOG00000019553	5 retrocopies	retro_dnov_1003, retro_dnov_2304, retro_dnov_2391, retro_dnov_441, retro_dnov_777,
Erinaceus europaeus	ENSEEUG00000011728	1 retrocopy	retro_eeur_107 ,
Felis catus	ENSFCAG00000027939	3 retrocopies	retro_fcat_482, retro_fcat_549, retro_fcat_649,
Microcebus murinus	ENSMICG00000009792	1 retrocopy	retro_mmur_744,
Mustela putorius furo	ENSMPUG00000002350	2 retrocopies	retro_mputfur_1406, retro_mputfur_166,
Otolemur garnettii	ENSOGAG00000015416	1 retrocopy	retro_ogar_1394,