RetrogeneDB ID: retro_eeur_154

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_104573:487..862(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: F11R
• Ensembl ID: ENSEEUG00000000928
• Aliases: None
• Description: F11 receptor [Source:HGNC Symbol;Acc:14685]

Sequence

>retro_eeur_154
TCCAAACCCACCATCAGTTTAGCATCCTCAGCCACATTGGCAGGTGCATGGTTGCTCATTTACTCAGATCCAGATGGGTC
TACAAGCTCCATGTACACTTGGTTCAAAGACGGGGAGAAGATGCCCAAGGACCCCAAGGACCAGCCAGGCTTTCAGCAAG
TCTTCCTATAGCCTGAACCCCAAGATGGGTGAGCTGGTCTTTGAGCCCCTGTAAGTCTCTGATTTGGGACAGTACTCCAG
CATGTCCTCCAATAGCTACAGGCCAGAGAACAAGTCAGAGGCCAAGAACATGGAGGCTGCAGAGCTGAATGTGCGGGGCA
TAGTGGCCACTGTGCTGCCCCCCTCATCCTCCTAGGACTGCTCATATCTAGTGCT

Alignment

ORF - retro_eeur_154 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.08 %
• Parental protein coverage: 73.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SKPTISIPSSATIGSRTVLTCSEPDGSPSSTYTWFKDGVKMPEDPK-TSRAFSNSSYNLNPKTGELVFEP
          SKPTIS..SSAT......L..S.PDGS.SS.YTWFKDG.KMP.DPK.TS.AFS.SSY.LNPK.GELVFEP
Retrocopy SKPTISLASSATLAGAWLLIYSDPDGSTSSMYTWFKDGEKMPKDPK>TSQAFSKSSYSLNPKMGELVFEP

Parental  LSASDSGQYSCTASNGYGPDTKSEAVNMEAAELNVGGIVAAVL-VTLILLGLLIFGA
          L..SD.GQYS...SN.Y.P..KSEA.NMEAAELNV.GIVA.VL...LILLGLLI..A
Retrocopy L*VSDLGQYSSMSSNSYRPENKSEAKNMEAAELNVRGIVATVL<APLILLGLLISSA

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	1.77 RPM
SRP017611_kidney	0.00 RPM	61.14 RPM
SRP017611_liver	0.00 RPM	55.63 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_154 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000000928	1 retrocopy	retro_eeur_154 ,
Echinops telfairi	ENSETEG00000016382	1 retrocopy	retro_etel_955,
Rattus norvegicus	ENSRNOG00000004414	1 retrocopy	retro_rnor_528,