RetrogeneDB ID: retro_eeur_504

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_330950:12555..12849(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OCIAD2
• Ensembl ID: ENSEEUG00000006759
• Aliases: None
• Description: OCIA domain containing 2 [Source:HGNC Symbol;Acc:28685]

Sequence

>retro_eeur_504
ATTACAAATATTATCTGAGTATGCCAAGAAGATAGCTTCTGGATGAGAGCCCTACCATTTTCTCTTGTGAGCATGCTTGT
CACCCAAGGACTCATCCACCAAGGTTATTTAGCATCAAACCCAAGATGTAGATGGTTGCTTAAAGTTGCACTTGCTGGTA
CCTTGGGATTTGGCCTTGGAAAGGCATCTAACATAAGAGTATGCCAGAAAAGATTCTACCTCTTTGAAGATCAGTTTCAT
GGAGCTGGTTTTGGTCCTGGACATAACAGGTTTGTGATCTGTTTATGTAACAAA

Alignment

ORF - retro_eeur_504 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.18 %
• Parental protein coverage: 74.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISKIIRECQEESFWKRALPFSLVSMLVTQGLVHQXXXXXXXXXXXXXXXXXAGILRFGLGRASYIRVCQK
          I..II..CQE.SFW.RALPFSLVSMLVTQGL.HQ.................AG.L.FGLG.AS.IRVCQK
Retrocopy ITNII*VCQEDSFWMRALPFSLVSMLVTQGLIHQGYLASNPRCRWLLKVALAGTLGFGLGKASNIRVCQK

Parental  KFHLFEEQLRGAGFGPGHNRHCLLTCEE
          .F.LFE.Q..GAGFGPGHNR.....C..
Retrocopy RFYLFEDQFHGAGFGPGHNRFVICLCNK

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	0.64 RPM	7.41 RPM
SRP017611_kidney	0.00 RPM	0.38 RPM
SRP017611_liver	0.00 RPM	0.00 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_504 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 13 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000018637	1 retrocopy	retro_cjac_1505,
Erinaceus europaeus	ENSEEUG00000006759	1 retrocopy	retro_eeur_504 ,
Homo sapiens	ENSG00000145247	1 retrocopy	retro_hsap_4082,
Gorilla gorilla	ENSGGOG00000013778	1 retrocopy	retro_ggor_2738,
Microcebus murinus	ENSMICG00000006147	1 retrocopy	retro_mmur_1402,
Macaca mulatta	ENSMMUG00000014869	1 retrocopy	retro_mmul_2353,
Monodelphis domestica	ENSMODG00000025531	1 retrocopy	retro_mdom_1006,
Nomascus leucogenys	ENSNLEG00000017430	1 retrocopy	retro_nleu_2048,
Oryctolagus cuniculus	ENSOCUG00000007907	2 retrocopies	retro_ocun_1734, retro_ocun_1780,
Otolemur garnettii	ENSOGAG00000011039	1 retrocopy	retro_ogar_561,
Pongo abelii	ENSPPYG00000014722	1 retrocopy	retro_pabe_3350,
Pan troglodytes	ENSPTRG00000016048	1 retrocopy	retro_ptro_2768,
Vicugna pacos	ENSVPAG00000011765	1 retrocopy	retro_vpac_331,