RetrogeneDB ID: retro_eeur_78

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_4669:6533..6794(+)
• Located in intron of: ENSEEUG00000012253

Retrocopy information

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

Parental gene information

• Parental gene symbol: ANAPC16
• Ensembl ID: ENSEEUG00000014902
• Aliases: None
• Description: anaphase promoting complex subunit 16 [Source:HGNC Symbol;Acc:26976]

Sequence

>retro_eeur_78
TCTGTCTCAGACCTGGCCCCACCACGGAAAGCCCATTTCACCTATCCCAAAGGAGCTGGTGAAATGTTAGAAGACGGCCC
TGAGTGATTCCTCTGTGAATCTGTTTTCAGCTACCAAGTGGCATCTATACTTAAACAAGTGAAGCATGATCAGCAAGTTG
TTTGGATGGAAAAACTAGTCGGTCTGGTAGAAGAGCTGGAGGCAGATGAGTGGCAATTTAAACCCATTAAGCAGCGGTTG
GGGTTCACACCCTCCTCAGGT

Alignment

ORF - retro_eeur_78 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.51 %
• Parental protein coverage: 79.09 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVSDLAPPRKALFTYPKGAGEMLEDGSERFLCESVFSYQVASTLKQVKHDQQVARMEKLAGLVEELEADE
          SVSDLAPPRKA.FTYPKGAGEMLEDG.E.FLCESVFSYQVAS.LKQVKHDQQV..MEKL.GLVEELEADE
Retrocopy SVSDLAPPRKAHFTYPKGAGEMLEDGPE*FLCESVFSYQVASILKQVKHDQQVVWMEKLVGLVEELEADE

Parental  WRFKPIEQLLGFTPSSG
          W.FKPI.Q.LGFTPSSG
Retrocopy WQFKPIKQRLGFTPSSG

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	14.34 RPM
SRP017611_kidney	0.00 RPM	20.44 RPM
SRP017611_liver	0.00 RPM	8.04 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_78 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014902	1 retrocopy	retro_eeur_78 ,
Felis catus	ENSFCAG00000010368	1 retrocopy	retro_fcat_390,
Microcebus murinus	ENSMICG00000004229	1 retrocopy	retro_mmur_2,
Oryctolagus cuniculus	ENSOCUG00000016767	1 retrocopy	retro_ocun_1674,
Otolemur garnettii	ENSOGAG00000008215	3 retrocopies	retro_ogar_1022, retro_ogar_1187, retro_ogar_135,