RetrogeneDB ID: retro_eeur_288

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_241628:764..1220(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000013677
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: EIF5
• Ensembl ID: ENSEEUG00000015883
• Aliases: None
• Description: eukaryotic translation initiation factor 5 [Source:HGNC Symbol;Acc:3299]

Sequence

>retro_eeur_288
AATAGTAACAGTGGTACAGGAAAGAAAGAGAAGGAAAAGAAAAACACAAAGTGCAAAGATAAGGAAAATGGCTCTGTGTC
CAACAGTGAAACACCACCACTTGCTCCACACAGTGAACTCAGTCCTCTTCCACATCTTGTGGAAGAAGAGGATTATGACT
GTGGAGAGGATACAACTGAGGAAGCTCAAAGGCACAGAATGGATTAAATTAGTGACCATGCAAAAGTTCTGACACTCAGT
GGTGATTTGGAAAGGATTGTGGAAGAGTGAGTTAACATCCTGTTTGATTTTGTTAAGAAAGAAAGAAGAAGGTATTATTG
ATTCATATGATAAGGAGATTGTTGCTGAAGTAGAGAGGCTGGATGTAAAAGCCATGGGTCCTCTTGTTTTGACGAAATTC
TTTTTAATGAGAAGATTATAGAACAAATTAAGAAGTGCAGGTACCATTTTCTACGA

Alignment

ORF - retro_eeur_288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.26 %
• Parental protein coverage: 54.45 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NSDSGTGKKEKEKKNRKGKDKENGSVSNSETPPPAPPNEISPPPHPVEEEDDDWGEDTTEEAQRRRMDEI
          NS.SG..................GSVSNSETPP.AP..E.SP.PH.VEEED.D.GEDTTEEAQR.RMD.I
Retrocopy NSNSGXXXXXXXXXXXXXXXXXXGSVSNSETPPLAPHSELSPLPHLVEEEDYDCGEDTTEEAQRHRMD*I

Parental  SDHAKVLTLSDDLERTIEERVNILFDFVK-KKKEEGIIDSSDKEIVAEAERLDVKAMGPLVLT-EVLFNE
          SDHAKVLTLS.DLER..EE.VNILFDFVK.KK.E.GIIDS.DKEIVAE.ERLDVKAMGPLVLT.E.LFNE
Retrocopy SDHAKVLTLSGDLERIVEE*VNILFDFVK>KKEE-GIIDSYDKEIVAEVERLDVKAMGPLVLT<EILFNE

Parental  KIREQIKKYRRHFLR
          KI.EQIKK.R.HFLR
Retrocopy KIIEQIKKCRYHFLR

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	9.99 RPM	75.25 RPM
SRP017611_kidney	9.75 RPM	70.51 RPM
SRP017611_liver	3.86 RPM	40.35 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_288 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001236	1 retrocopy	retro_cpor_577,
Erinaceus europaeus	ENSEEUG00000015883	1 retrocopy	retro_eeur_288 ,
Monodelphis domestica	ENSMODG00000013424	1 retrocopy	retro_mdom_2000,
Rattus norvegicus	ENSRNOG00000010218	2 retrocopies	retro_rnor_1781, retro_rnor_2459,