RetrogeneDB ID: retro_eeur_688

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_72893:352..903(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000010044
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ABHD17B
• Ensembl ID: ENSEEUG00000013750
• Aliases: None
• Description: abhydrolase domain containing 17B [Source:HGNC Symbol;Acc:24278]

Sequence

>retro_eeur_688
CTGCAGCTGGGTGAGCGCGCTGACTTCCAGTATGGCCAGCGCAAGCTGGACAACATCGAGGTCTTCGTGACCAAGAGCAG
CCGCGGCAACCTCGTGGCCTGCATGTACGTGCGCTGCCCACCGGAGCCAGGTGCACACTGCTCTTCTCACACGGCTACGC
AGTGGACCTGGGCCAGATGAGCCGCTTCTACGTGGGCCTGGGCTCCCACTGTGGCTGCAACATCCTCTCCTATGACTACT
CGTCCGGGCTATCGGGCCGGCCCTCTGAGAAGAACCTGTAGGCAGACATTGACGCTGCCGTCTGGCAGGTGCTGCGCACG
AGGTACGGGATCAGCCCCGACAGCGTGGTGCTATATGGCCAGAGCATCCGCACGGTGCCCACCGAGGGCTTGGCGGCCCG
AACTGAGTGAGCTGCGGTGGTGCTGCACTCGCCACTCACGTCGGGCATTCGGGTAGCCTTCCCCGACACCACGAAGACCT
ACTGCCTCGACGCCTCCCCCAACATCTAGAAGGTGTCCCGCATCTCATCGCTGGTTTTGCTGATCCACGGC

Alignment

ORF - retro_eeur_688 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.31 %
• Parental protein coverage: 63.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LHLSERADWQYSSREKDAIECFMTRTSKGNRIACMFVRCSPN-AKYTLLFSHGNAVDLGQMSSFYIGLGS
          L.L.ERAD.QY..R..D.IE.F.T..S.GN..ACM.VRC.P..A..TLLFSHG.AVDLGQMS.FY.GLGS
Retrocopy LQLGERADFQYGQRKLDNIEVFVTKSSRGNLVACMYVRCPPE<ARCTLLFSHGYAVDLGQMSRFYVGLGS

Parental  RIIC-IFSYDYSGYGPSSGKPTEKNLYADIEAA-WLALRTRYGIRPENVIIYGQSIGTVPSVDLAARYES
          ...C.I.SYDYS.....SG.P.EKNL.ADI.AA.W..LRTRYGI.P..V..YGQSI.TVP...LAAR.E.
Retrocopy HCGCNILSYDYSS--GLSGRPSEKNL*ADIDAAVWQVLRTRYGISPDSVVLYGQSIRTVPTEGLAARTE*

Parental  AAVILHSPLTSGMRVAFPDTKKTYCFDAFPNIDKISKITSPVLIIHG
          AAV.LHSPLTSG.RVAFPDT.KTYC.DA.PNI.K.S.I.S.VL.IHG
Retrocopy AAVVLHSPLTSGIRVAFPDTTKTYCLDASPNI*KVSRISSLVLLIHG

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	38.19 RPM
SRP017611_kidney	0.00 RPM	17.25 RPM
SRP017611_liver	0.00 RPM	14.15 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_688 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
Ailuropoda melanoleuca	ENSAMEG00000007245	1 retrocopy	retro_amel_1787,
Erinaceus europaeus	ENSEEUG00000001302	1 retrocopy	retro_eeur_265,
Erinaceus europaeus	ENSEEUG00000013750	1 retrocopy	retro_eeur_688 ,