RetrogeneDB ID: retro_eeur_343

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_264600:3799..4237(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000010266
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: VDAC2
• Ensembl ID: ENSEEUG00000008623
• Aliases: None
• Description: voltage-dependent anion channel 2 [Source:HGNC Symbol;Acc:12672]

Sequence

>retro_eeur_343
TGCCAGCGGCCAGTGTGTACTCCTCCAGCATACGCTGACCTTGGCAAAGCTGCCAGAGATATTTTCAACAAACGCTTTGG
TTTTGGGTTGGTGAAACTGGATGTGAAAAAAAAGTCATGCCATGGCGTAGGATTTTCAAGACCTGGTTCATCTAATACAG
ACACTGGTAACGTTACTGGGACCTTGGAGACCAAAGATAAATGGTGTGAGTATATTCTGACTTTCACAGACCAATGGAAC
ACTGATAACACACTGGGAACAGAAACTGCAACTGAAGACCAGATTTGCCATGGTTTAAAACTGACATTTGATACCACCTC
TTCACTAAACATGGGAAAGGAACGTGGTAAAAGCAAGTCTTCTCACAAGAGGGAGTGCATAAACCTTGGTTGTGACGTTG
ACTTCCATTTTGCTGGACCTGCAATCCAGGGTTCGTCC

Alignment

ORF - retro_eeur_343 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.23 %
• Parental protein coverage: 56.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  CHVTMCIPPSYADLGKAARDIFNKGFXXXXXXXXXXXXXXXXXEFSTSGSSNTDTGKVTGTLETKYKWCE
          C....C.PP.YADLGKAARDIFNK.F.........XXX......FS..GSSNTDTG.VTGTLETK.KWCE
Retrocopy CQRPVCTPPAYADLGKAARDIFNKRFGFGLVKLDVXXXSCHGVGFSRPGSSNTDTGNVTGTLETKDKWCE

Parental  YGLTFTEKWNTDNTLGTEIAIEDQICQGLKLTFDTTFSPNTGKKSGKIKSSYKRECINLGCDVDFDFAGP
          Y.LTFT..WNTDNTLGTE.A.EDQIC.GLKLTFDTT.S.N.GK..GK.KSS.KRECINLGCDVDF.FAGP
Retrocopy YILTFTDQWNTDNTLGTETATEDQICHGLKLTFDTTSSLNMGKERGKSKSSHKRECINLGCDVDFHFAGP

Parental  AIHGSA
          AI.GS.
Retrocopy AIQGSS

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	150.35 RPM
SRP017611_kidney	0.00 RPM	322.38 RPM
SRP017611_liver	0.00 RPM	92.45 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_343 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008623	2 retrocopies	retro_eeur_192, retro_eeur_343 ,
Nomascus leucogenys	ENSNLEG00000016857	1 retrocopy	retro_nleu_1608,
Rattus norvegicus	ENSRNOG00000013505	1 retrocopy	retro_rnor_2652,
Tupaia belangeri	ENSTBEG00000001946	4 retrocopies	retro_tbel_1504, retro_tbel_1541, retro_tbel_1885, retro_tbel_4597,
Vicugna pacos	ENSVPAG00000008068	1 retrocopy	retro_vpac_156,