RetrogeneDB ID: retro_eeur_134

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_8443:420768..421049(+)
• Located in intron of: ENSEEUG00000004720

Retrocopy information

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

Parental gene information

• Parental gene symbol: DYNLRB2
• Ensembl ID: ENSEEUG00000013344
• Aliases: None
• Description: dynein, light chain, roadblock-type 2 [Source:HGNC Symbol;Acc:15467]

Sequence

>retro_eeur_134
ATGGCAGAAGTAGAGGAGACACTGAAATGACTTCAGAGCCAAAAAGGAGTGCAGTGCATCATCTTGGTGAACACAGAAGG
CATTCCCATCAAAAGCACTATGGACAAACCCACCACCACACAATATGCCAACCTATGTACAACTTCATCCTGAAGACCTA
GAGCACCATGTGCAAAATTGACCCACAGAATGATCTCACCTTTCTTCGAATTCACTCCAAGAAAAATGAAGTTATAGTTG
CACTAGATAAAGACTATTTCCTGATTGTGATTCAGAATCCA

Alignment

ORF - retro_eeur_134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.11 %
• Parental protein coverage: 97.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTEVEETLKRIQSHKGVIGTMVVNAEGIPIRTTLDNSTTVQYAGL-LHQLTMKARSTVRDIDPQNDLTFL
          M.EVEETLK..QS.KGV.....VN.EGIPI..T.D..TT.QYA.L.......K..ST...IDPQNDLTFL
Retrocopy MAEVEETLK*LQSQKGVQCIILVNTEGIPIKSTMDKPTTTQYANL<MYNFILKT*STMCKIDPQNDLTFL

Parental  RIRSKKHEIMVAPDKEYLLIVIQNP
          RI.SKK.E..VA.DK.Y.LIVIQNP
Retrocopy RIHSKKNEVIVALDKDYFLIVIQNP

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	10.47 RPM	5.96 RPM
SRP017611_kidney	21.19 RPM	2.81 RPM
SRP017611_liver	7.23 RPM	0.16 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_134 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000020024	1 retrocopy	retro_cfam_575,
Erinaceus europaeus	ENSEEUG00000013344	2 retrocopies	retro_eeur_134 , retro_eeur_552,
Sarcophilus harrisii	ENSSHAG00000002755	1 retrocopy	retro_shar_421,