RetrogeneDB ID: retro_eeur_397

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_283344:2016..2526(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM221A
• Ensembl ID: ENSEEUG00000001634
• Aliases: None
• Description: family with sequence similarity 221, member A [Source:HGNC Symbol;Acc:27977]

Sequence

>retro_eeur_397
GGGAAACATTTTACTCCTGAGGAATATGAAAATTACAAAAGAAAACTTTTACAGAACAGATTATTTGTGAACTGGCGATC
ACCAACTGGAATGGACTGTAAACTTGTGGGTCCAGAGACACTGTGTTTTCGTACGCACAGGTATAAGCAACATGATACTG
ACTTTGAAATGATTCCACAACAGCGCCCCATTAGCTTGCTTTGCTGAGTGCCTGGCTGCCAGTGCAGGGCTTACCTTTAC
ATCTCTACGAATGGCACGCAGCCCATTCGCTGCAGGTGCAAGCACTTTGTTGATCAGCACAGTGCTGCACCTGGATCCAA
ATGCAATGCCTGCCCCGAGTGTTCAGGATTCCACAGCTCCTTCACTTGTGGTTTTGGCTATCCCTCATATGCCCATGACA
CAGTTGTAGAAACTAAGCAAGAAAGACTGGCTCAAGGAAGACCAGTGGGAGAAGACATTCTTTATGCAGCTATGCGAGGA
TTAACTGGCTTCAGCTCACTGGCAGACGGC

Alignment

ORF - retro_eeur_397 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.18 %
• Parental protein coverage: 62.82 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GKLFTPEEYEDYKRKVLPMRLQNRLFVSWRSPTGIDCKLVGPETLCFCTHRYKQHKTDFETIPQQRPISL
          GK.FTPEEYE.YKRK.....LQNRLFV.WRSPTG.DCKLVGPETLCF.THRYKQH.TDFE.IPQQRPISL
Retrocopy GKHFTPEEYENYKRKL----LQNRLFVNWRSPTGMDCKLVGPETLCFRTHRYKQHDTDFEMIPQQRPISL

Parental  PCRVTGCQCRAYLYVPMNGTQPIRCRCKHFADQHSAAPGSKCNACSKCSGFHSCFTCGCGQPAYAHDTVV
          .C.V.GCQCRAYLY...NGTQPIRCRCKHF.DQHSAAPGSKCNAC..CSGFHS.FTCG.G.P.YAHDTVV
Retrocopy LC*VPGCQCRAYLYISTNGTQPIRCRCKHFVDQHSAAPGSKCNACPECSGFHSSFTCGFGYPSYAHDTVV

Parental  ETKQERLALGKPVGQDIPYAAMGGLTGFSSLAEG
          ETKQERLA.G.PVG.DI.YAAM.GLTGFSSLA.G
Retrocopy ETKQERLAQGRPVGEDILYAAMRGLTGFSSLADG

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	2.26 RPM
SRP017611_kidney	0.00 RPM	5.81 RPM
SRP017611_liver	0.00 RPM	4.02 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_397 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002784	1 retrocopy	retro_cfam_1852,
Erinaceus europaeus	ENSEEUG00000001634	2 retrocopies	retro_eeur_349, retro_eeur_397 ,