RetrogeneDB ID: retro_eeur_46

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2596:12094..13191(-)
• Located in intron of: ENSEEUG00000009499

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000004189
• Aliases: None
• Description: None

Sequence

>retro_eeur_46
TTCAAAGCTGTGATGGATGGAATTGATGTCCTGATCAAGCAGAAAGTTTCCCCCAGCAGGTGCAGATTACAAGTGCTGGA
TTTACAGTTCACTGGGCAGAAGTTCTGGAACACATGGACTGGAACCCACCTCCAAGCATACTCACAAAAGAGAGAACTGA
TGCCTGAGGGAACTTCAAAGAAAGAGAAGGCCACACCCTACTTGGAGGTGTGTGTAGACCTCTACCTTGGTGAAGAACAA
GTTGATAGGTTTTCCACCTACTTGCTGAACTGGACCAAAAAAAGAAAGGGAGTACACCTTTCCTATAAGACAGTAAGGAT
ACATTACCTGACCAGAAAGTATTTCAGGTTTCTGTATGCCGTGTCATGCTGTGACATCATGGAGCTGGGAATCCATTGTA
CCTTGCCATTCTCCACCCTGCGCATGCTTGCTAACCTGCTGGGCATGCTGAGTAATCTCAAGAGACTGGTGGTCTGCATC
AAGATTCCTATTGCAACCACCCCAGAAAAGGCAGAATGGAGGTTGCTATCTATCAACAATTTCACATCTGAATGCTCCCA
GCTACTTCATCTTCAAGAGCTGTACCTGGAATCTCCCTCCTTCCTCAGGGATCATCTGCACTGTCTGTTCAGGTGTTTTA
ATACCTCCTTGGAGGTCTTCTCACTCACTAACTGCAGATTTAGAAAAAAAATATTGACTCACGTGTTCCAAAGCCCATGT
ATCAGTCAACTGAAGGACCTGTGTCTGAAGGGAGTCCCCTTAACCTCAGTCGGTAAGTGTCTGCGATCTCTGCTGGAGAT
AAATGCAGCCACCCTCCAGCACCTGGACCTGGGTCTGTGTGGCCTCCAGGACCCCTGGCTTGAGGCCCTGCTCCCTGCCC
TGAGCAGCTGCTCGCAGCTCAGATCCTTCAGCCTGCATGGGAACCGCCTGTCCATGGCCACTCTGGAGAAGCTGCTGAGA
TGTACCTCGGGCCTCAGCAGGTTAAAACTAGAGCTCTATCCGGCCCCTCTGGAGAGTTTCAGCCCACAGGGAGTTTTGCA
GCCTGCACATTTAGGTTGCATTGTACTCAGATCATAAAGATTCTCAAGGACCTTAGA

Alignment

ORF - retro_eeur_46 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.76 %
• Parental protein coverage: 77.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FKAVMDGIDVLLKQEVPHSRCKLRVLDLQFTGQKFWRMWTGTSQVFRKEKTVDDLQGTRRQ----PYFEV
          FKAVMDGIDVL.KQ.V..SRC.L.VLDLQFTGQKFW..WTGT.......K......GT.......PY.EV
Retrocopy FKAVMDGIDVLIKQKVSPSRCRLQVLDLQFTGQKFWNTWTGTHLQAYSQKRELMPEGTSKKEKATPYLEV

Parental  CVDLYISKP--DRLSNYLLDWIRERKGVHLSCKTVMIYSLTRKSFRFLHAMPFCDIKELGIHCTLTFSTL
          CVDLY......DR.S.YLL.W...RKGVHLS.KTV.I..LTRK.FRFL.A...CDI.ELGIHCTL.FSTL
Retrocopy CVDLYLGEEQVDRFSTYLLNWTKKRKGVHLSYKTVRIHYLTRKYFRFLYAVSCCDIMELGIHCTLPFSTL

Parental  RLLGIQLGMMNNLKRLDVCIDI-LCNHPD--DWMPVCISEFTSAFHQLLHLQELYLKSPFFLQGHLHQLI
          R.L...LGM..NLKRL.VCI.I.....P....W....I..FTS...QLLHLQELYL.SP.FL..HLH.L.
Retrocopy RMLANLLGMLSNLKRLVVCIKIPIATTPEKAEWRLLSINNFTSECSQLLHLQELYLESPSFLRDHLHCLF

Parental  RSLATPLEVFSLTNCRVTEGDLTHLFQSPHITHLKDLCLRGLPLTSVSEPLRALLEVNAATLQHLDLGLC
          R...T.LEVFSLTNCR.....LTH.FQSP.I..LKDLCL.G.PLTSV...LR.LLE.NAATLQHLDLGLC
Retrocopy RCFNTSLEVFSLTNCRFXXXXLTHVFQSPCISQLKDLCLKGVPLTSVGKCLRSLLEINAATLQHLDLGLC

Parental  GLQDPQLEALLPALSSCSQLSSLSLHGNRLSMATLEKLLRCTSGLSRLRQEIYPAPMETFNPQGILQPQ-
          GLQDP.LEALLPALSSCSQL.S.SLHGNRLSMATLEKLLRCTSGLSRL..E.YPAP.E.F.PQG.LQP..
Retrocopy GLQDPWLEALLPALSSCSQLRSFSLHGNRLSMATLEKLLRCTSGLSRLKLELYPAPLESFSPQGVLQPA<

Parental  TFDLLCTHIFKILKELK
          TF.L.CT.I.KILK.L.
Retrocopy TFRLHCTQIIKILKDLR

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.00 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_46 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	ENSEEUG00000004189	1 retrocopy	retro_eeur_46 ,