RetrogeneDB ID: retro_eeur_388

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_279923:13794..14742(-)
• Located in intron of: ENSEEUG00000010753

Retrocopy information

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

Parental gene information

• Parental gene symbol: SLC35F5
• Ensembl ID: ENSEEUG00000003303
• Aliases: None
• Description: solute carrier family 35, member F5 [Source:HGNC Symbol;Acc:23617]

Sequence

>retro_eeur_388
GTGCTGAGCTCTTCACCTCCTTTTAGACTCAGCTCTACCAAGTTTTCAGGTTTTGCCCTTGAAGATCTCAGAAAGGCCTT
TAACATTAAGACTGCGAATGCTGTGTGTGTTTATCATGAACCGATTGAATTCCCAGAGCAGTAGTTTCAGTCAATGCAGG
AGAATGGCTCTTGGGATTGTTACTCTTCTTGTTGATGTGATATGGGTGGCATCCTCTGAACTTACGTCTTAGGTTTTTAC
TCAGTACAACAAACCATTCTTCAGCACCTTTGCAAAAACATCAATGTTTGTTCTCTACCTTTTGGGTTTTATTGTTTGGA
AGCCATGGAGACAGCAGTGTACAGGAAGATTTCGAGGAAAGCATGCTGCTTTTTTTTTAACAGATGCTGAAGGCTACTTT
GCTGCTTGCTCAACAGACACAACTATTAACAATTCGTTGAGTGAGCCCTTATATGTTCCTGTGAAGTTTCATGATCTTCC
AAGTGAAAAATCTGAGAACACAAATATTGACACTGAAAAAACTCCCAAAAAGTCTCGTGTAAGGTTCACTAATATCATGG
AGATTTGACAACTTCCGTCAAGCCATGCATTGGAAGCTAAGTTGTCTCCCATGTCATACCCTACTGTGAAAGAACAAGAA
TTTTTACTCAAAACTGTTGGAAAACTTAACTGCCACTCAAGTAGCAAAAATTAGTGTTTTTTTTTTTCTTTGTGTGGTTT
TTGGCGAATTTGTCATATCAAGAAGCTCTTTCAGACACACAAACTGCTATAGTTAATATTTTATCTTCAACTTCTGGACT
TTTTCCCCTAATTCTTGCTGCAGTGTTTCCAAATAACAGTGGCGATAGATTTATTCTTCCTAAACTATTAGCTATGATTT
TAAGTATTGGATGCATTGTGCTGGTAAACCTGTCAGGGTCTGAAAAATCTGCTGGAAGAGATACAATA

Alignment

ORF - retro_eeur_388 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 76.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VLSSSPPFRLSSAKFSGFALEDLRKAFNI-RLQMLCVFIMNRLNSQSSGFSQRRRMALGIVILLLVDVIW
          VLSSSPPFRLSS.KFSGFALEDLRKAFNI.RL.MLCVFIMNRLNSQSS.FSQ.RRMALGIV.LL.VDVIW
Retrocopy VLSSSPPFRLSSTKFSGFALEDLRKAFNI>RLRMLCVFIMNRLNSQSSSFSQCRRMALGIVTLL-VDVIW

Parental  VASSELTSYVFTQYNKPFFSTFAKTSMFVLYLLGFIVWKPWRQQCTRRFRGKHAAFF-TDAEGYFAACST
          VASSELTS.VFTQYNKPFFSTFAKTSMFVLYLLGFIVWKPWRQQCT.RFRGKHA....TDAEGYFAACST
Retrocopy VASSELTS*VFTQYNKPFFSTFAKTSMFVLYLLGFIVWKPWRQQCTGRFRGKHAXXXXTDAEGYFAACST

Parental  DTTINSSLREPLYVPV-FHDLPKEKSWNLNIDTEKTPKKSRVRFSNIMEIRQLPSSHALEAKLSRMSYPT
          DTTIN.SL.EPLYVPV.FHDLP.EKS.N.NIDTEKTPKKSRVRF.NIMEI.QLPSSHALEAKLS.MSYPT
Retrocopy DTTINNSLSEPLYVPVKFHDLPSEKSENTNIDTEKTPKKSRVRFTNIMEI*QLPSSHALEAKLSPMSYPT

Parental  VKEQEFLLKTVGKL-TATQVAKISFFFC-FVWFLANLSYQEALSDTQVAIVNILSSTSGLFTLILAAVFP
          VKEQEFLLKTVGKL.TATQVAKIS.....FVWFLANLSYQEALSDTQ.AIVNILSSTSGLF.LILAAVFP
Retrocopy VKEQEFLLKTVGKL>TATQVAKISXXXX>FVWFLANLSYQEALSDTQTAIVNILSSTSGLFPLILAAVFP

Parental  SNSGDRFTLSKLLAVILSIGGVVLVNLSGSEKSAGRDTI
          .NSGDRF.L.KLLA.ILSIG..VLVNLSGSEKSAGRDTI
Retrocopy NNSGDRFILPKLLAMILSIGCIVLVNLSGSEKSAGRDTI

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	1.45 RPM	10.15 RPM
SRP017611_kidney	10.13 RPM	59.82 RPM
SRP017611_liver	3.05 RPM	14.47 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_388 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013643	1 retrocopy	retro_dnov_1887,
Erinaceus europaeus	ENSEEUG00000003303	1 retrocopy	retro_eeur_388 ,