RetrogeneDB ID: retro_eeur_393

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_282445:5910..6500(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ASPA
• Ensembl ID: ENSEEUG00000000496
• Aliases: None
• Description: aspartoacylase [Source:HGNC Symbol;Acc:756]

Sequence

>retro_eeur_393
ATTTTTGGCCTTCATAATGCTACTTCTAACATGGGATGCACTCTTATTATTGAAGATTCCAGGAATGAATTTTAATTCAG
GTGTTTCATTACATTAAGACTTCCTTGGCTCCATCACCCTGCTATGTTTATCTTTTGGAGCATCCTTCCCTCAAATACGC
AACCCCACATTCTATAGCCAAGTATCCTGTTGGCATAGAAGCTGGTCCCCATCCTCAAGGGGTTCTGAGAGCTGATATTT
TTGATCAAGTGAGAACAAATAATAAGTATGTCCTTGATTTTATACATAACTTCAATACAGGAAAATAACTTCCTCCATGT
GCTACTGAAATCTATAAGATAATAGAGAAAGTTGATTATCCTGGGAATAAAAATGGATAAATTATTGCTGTTATCCATGC
TAATCTGCAGGATTAAGACAGGAAACTACTGTGCCCTGGGAATCTCATGCTTTGAACACTTGATGAAAAGACTATTCCAC
TGGGTGGTGACTGTATTGTGTACCCAGTGTTTGTAAACAAGGCTGCATATGATGAAAAGAAAGAAGCTTTGGCAAAAATA
ACTGAACACTCAGCACAAAAGAGTATTCAC

Alignment

ORF - retro_eeur_393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.87 %
• Parental protein coverage: 63.46 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IFDLHNTTANMGCTLILEDSRNNF-LIQMFHYIKTSLAPLPCYVYLTEHPSLKYATTRSIAKYPVGIEVG
          IF.LHN.T.NMGCTLI.EDSRN.F.LIQ.FHYIKTSLAP.PCYVYL.EHPSLKYAT..SIAKYPVGIE.G
Retrocopy IFGLHNATSNMGCTLIIEDSRNEF<LIQVFHYIKTSLAPSPCYVYLLEHPSLKYATPHSIAKYPVGIEAG

Parental  PQPQGVLRADILDQMRKIIKHALDFIQKFNTGKEFPPCAIEVYKIIEKVDYPRNENGEIIAVIHPNLQDQ
          P.PQGVLRADI.DQ.R...K..LDFI..FNTGK..PPCA.E.YKIIEKVDYP.N.NG.IIAVIH.NLQD.
Retrocopy PHPQGVLRADIFDQVRTNNKYVLDFIHNFNTGK*LPPCATEIYKIIEKVDYPGNKNG*IIAVIHANLQD*

Parental  DWKPLRPGDPVFLTLDGKTIPLGGDCIVYPVFVNEAAYYEKKEAFAKTTKLTLNAKSIH
          D.K.L.PG.....TLD.KTIPLGGDCIVYPVFVN.AAY.EKKEA.AK.T......KSIH
Retrocopy DRKLLCPGNLML*TLDEKTIPLGGDCIVYPVFVNKAAYDEKKEALAKITEHSAQ-KSIH

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	3.71 RPM
SRP017611_kidney	0.00 RPM	109.90 RPM
SRP017611_liver	0.00 RPM	41.00 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_393 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000000496	1 retrocopy	retro_eeur_393 ,