RetrogeneDB ID: retro_eeur_291

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_2429:3864..6261(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCDHGA1
• Ensembl ID: ENSEEUG00000002556
• Aliases: None
• Description: protocadherin gamma subfamily A, 1 [Source:HGNC Symbol;Acc:8696]

Sequence

>retro_eeur_291
AGGCTGATCCCGCTGTGCCTGCTTTGGGCGGCCCTGTGGGAAACCGGAGCCGGGCTGATGCGCTATTCTGTGCCAGAAGA
GATCGACAAAGGCTCCTTTGTGGGCAACATCGCCAAGGATTTGGGTTTGGAGGCCCCAGTGCTGGTGCAGCGCGGAGTCC
GCATCGTCTCCCGAGGTAGGACGCAGCTCTTTGCTCTGCACCCGCGCAGCGGCAGCTTGGTCACCGCGGGCAGGATCGAC
CGCGAGGAGCTCTGCGCTCAGAGCGCTCGGTGCCTGGTGAACTTTAACATCCTGATGGAAGACACATTGAATATTTACTC
AGTAGAGGTGGAAATAACAGATATTAACGACAGTGCACCTCGCTTTGGAGTAGATGAACTGGAGGTAAAGATCAGTGAAT
TAACTACAGCTGGATTCAGGATTCCTCTAAAGACTGCTCATGATGCAGACGTGGGGAAAAACGGTCTGCAGAAATACCAG
CTGAACCCAAATGACCACTTCTCCCTGGACGTGCAGAGCGGCGTGGATGGGAACAAGTTCCCGGAGCTGGTGCTGGAGCA
GGCCCTGGATCGCGAGGAAGAAACCACTCACCATCTTGTCCTCACAGCTTTGGATGGAGGCGACCCGGTGCTATCTGGTA
CCTCCCGCATCCGCGTGGTGGTCCTGGATGCTAACGACAACGCACCCCTGTTCACACAGCCCGAGTACCATGTAAGTGTT
CCAGAGGATAAGCCCATAGGCACCCGCATACTCACGGTGACCGCCACTGATGTAGATGAGGGGTACAATGCTCAAGTGGC
ATATTTTCAGGAGAAAAGCCCTGATGAGACCACAGAGGTCTTTGAGCTGAAGTCCACATCTGGAGAAATAACACTTACCA
GAAGACTTGATTATGAGGATGCCAAATTCCACGAAATTGATATTGAAGCACGTGATGGCCCTGGCCTCCTGACCAGAGCG
AAGGTTATTGTCACAGTTTTGGACGTAAATGACAACGCCCCTGAATTTTACATGACATCTGTCAGTAGCTCAGTTCCTGA
AGACTCTCCTCCAGGCACTGTAATTGCACTTTTCAATGTCCATGACAGAGACTCTGGGCAGAATGCACTTATTACATGCT
CACTCCCAGACAACCTTCCTTTCAAGCTGGAAAGGTCAGTGGACAATTACCACCGACTGGTTACAACCAGAGCCCTTGAC
AGGGAACAGTTTTCCTCTTACAACATCACTGTGACAGCCAGAGATGGAGGAGACCCATCCCTGTCTACCAAGGCTCATGT
TTGGCTGCAGGTGGCAGACATCAATGACAACCCACCTGCCTTCCCTCAAGCTTCCTACTCTGCCTACATTCCTGAAAACA
ACCTCAGAGGTGCTTCTATCTTTGCCCTGATGGCCCAGGACCCTGACTCTGAGGACAATGCCCATGTCACTTATAGCTTG
ACTGAGGACAGCGTTCAGGGGGCACCTCTGTCCTCCTACATCTCCATCAACACTGACATAGGAGTCCTCTATGCTTTGTG
TTCCTTTGACTATGAGCAGTTCCGTGAACTACAGCTATGGGTGACAGCAATGGACAGTGGGAAGCCTCCACTCAGCAGCA
ATGTGTCCCTGAGGCTGTTCATTCTGGACCAGAATGACAATGTTCCTGAGATCTTGTACCCCACCCTCCCCACTGATGGT
TCCACAGGAGTGGAGCTGGCACCCCGCTCTGCAGAGCCCGGATACCTGGTGACCAAGGTGGTGGCAGTGGACAGAGACTC
AGGCCAGAATGCCTGGCTGTCCTACCGCCTGCTCAAGGCCAGTGAGCCAGGGCTCTTCTCAGTGGGGCTGCACACAGGTG
AGGTGCACACTGCCAGGGCCCTGCTGGACAGAGATGCTCTCAAGCAGAGCCTGGTGGTGGCAGTGCAGGACCATGGCCAG
CCCCCTCTCTCAGCCACTGTCACACTCACTGTGGCCATAGCTGACAGCATCCCAGATGTGCTGGCTGACCTGGGCAGCCT
GGAGTCTCCTGCCAATCCTGAAGATTCTGACCTCACACTCTACCTGGTGGTGGCACTAGCCTCTGTGTCCTGCATCTTCC
TTGCCTTTGTCATCGTGCTGCTGGCTGTCAGGCTGAGGCGCTGGCACACATCCCGCCTGCTCCAGGCTTCAGCAGGTGGA
CTGGCTGGCCTTCCTGCCTCTCACTTTGTGGGTATGGATGGGGTGCAGGCTTTCCTACAGACCTATTCCCATGAGGTGTC
CCTCACTGCAGACTCCAGGAAGAGTCACCTGATCTTCCCCCAGCCCAACTATGCTGACACCCTCATCAGCCAGGACAGCT
GTGAGAAAAGGGAATTTCTGTCAAATCCTCAATCTCTACTTGAAGATAAAGGAGCAGAACCATTTTCTCAGGTAAAT

Alignment

ORF - retro_eeur_291 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.22 %
• Parental protein coverage: 97.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLVQLCLFVGLLLEVQAGKILYFVPEETVKGFFVGSIAKDLGLQAQELAGRGIRIVSRGRTQLFALNPRS
          RL..LCL....L.E..AG...Y.VPEE..KG.FVG.IAKDLGL.A..L..RG.RIVSRGRTQLFAL.PRS
Retrocopy RLIPLCLLWAALWETGAGLMRYSVPEEIDKGSFVGNIAKDLGLEAPVLVQRGVRIVSRGRTQLFALHPRS

Parental  GSLVTAGRIDREELCAQSARCLVSFNILVEDKMKLFPIEVEILDINDNAPHFQIEELELKMNEITSPGTR
          GSLVTAGRIDREELCAQSARCLV.FNIL.ED.......EVEI.DIND.AP.F...ELE.K..E.T..G.R
Retrocopy GSLVTAGRIDREELCAQSARCLVNFNILMEDTLNIYSVEVEITDINDSAPRFGVDELEVKISELTTAGFR

Parental  IPLPFGQDFDVGVNSLQSYQLSSNPHFFLDVQQGADGLQHPEMVLQSPLDREQEAVHHLVLTASDGGDPV
          IPL....D.DVG.N.LQ.YQL..N.HF.LDVQ.G.DG...PE.VL...LDRE.E..HHLVLTA.DGGDPV
Retrocopy IPLKTAHDADVGKNGLQKYQLNPNDHFSLDVQSGVDGNKFPELVLEQALDREEETTHHLVLTALDGGDPV

Parental  RSGMLRIHVQVVDANVNPPTFTQAQYQVSVLENVPLGTQLLTVKATDPDEGANGEVTYAFHNIDHRVAQI
          .SG..RI.V.V.DAN.N.P.FTQ..Y.VSV.E..P.GT..LTV.ATD.DEG.N..V.Y............
Retrocopy LSGTSRIRVVVLDANDNAPLFTQPEYHVSVPEDKPIGTRILTVTATDVDEGYNAQVAYFQEKSPDETTEV

Parental  FQLDPHMGEITNKEPLDFEEYNLYPMEIQAQDGAGLMARAKVLVKVLDINDNAPEVTITSVTASVPENFP
          F.L....GEIT....LD.E........I.A.DG.GL..RAKV.V.VLD.NDNAPE...TSV..SVPE..P
Retrocopy FELKSTSGEITLTRRLDYEDAKFHEIDIEARDGPGLLTRAKVIVTVLDVNDNAPEFYMTSVSSSVPEDSP

Parental  PGTIIALINVHDQDSGDNGHTTCSISRNLPFKLEKLVDNYYRLVTEKTLDRELTPTYNITVTATDQGTPA
          PGT.IAL.NVHD.DSG.N...TCS...NLPFKLE..VDNY.RLVT...LDRE....YNITVTA.D.G.P.
Retrocopy PGTVIALFNVHDRDSGQNALITCSLPDNLPFKLERSVDNYHRLVTTRALDREQFSSYNITVTARDGGDPS

Parental  LSTEAHISLHITDINDNSPVFSQDSYSAYIPENNPRGASIFSVTAHDADSNENAQVNYFLAEDDILGAPL
          LST.AH..L...DINDN.P.F.Q.SYSAYIPENN.RGASIF...A.D.DS..NA.V.Y.L.ED...GAPL
Retrocopy LSTKAHVWLQVADINDNPPAFPQASYSAYIPENNLRGASIFALMAQDPDSEDNAHVTYSLTEDSVQGAPL

Parental  SSYVSINSDIGVLYALCSFDYEQFRELQLWVTALDSGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDG
          SSY.SIN.DIGVLYALCSFDYEQFRELQLWVTA.DSGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDG
Retrocopy SSYISINTDIGVLYALCSFDYEQFRELQLWVTAMDSGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDG

Parental  STGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQS
          STGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQS
Retrocopy STGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQS

Parental  LVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPGDSDLTLYLVVAVAVVSCVFLAFVIVL
          LVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPA.P.DSDLTLYLVVA.A.VSC.FLAFVIVL
Retrocopy LVVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPANPEDSDLTLYLVVALASVSCIFLAFVIVL

Parental  LAVRLRRWHTSRLLQASAGELAGLPASHFVGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLIS
          LAVRLRRWHTSRLLQASAG.LAGLPASHFVG.DGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLIS
Retrocopy LAVRLRRWHTSRLLQASAGGLAGLPASHFVGMDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLIS

Parental  QESCEKREFLSAPQSSLED-SKETFSQVN
          Q.SCEKREFLS.PQS.LED...E.FSQVN
Retrocopy QDSCEKREFLSNPQSLLEDKGAEPFSQVN

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	5.16 RPM	6.77 RPM
SRP017611_kidney	0.75 RPM	0.75 RPM
SRP017611_liver	0.64 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_291 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000002556	6 retrocopies	retro_eeur_140, retro_eeur_291 , retro_eeur_527, retro_eeur_630, retro_eeur_631, retro_eeur_637,
Ficedula albicollis	ENSFALG00000008476	1 retrocopy	retro_falb_10,
Pelodiscus sinensis	ENSPSIG00000004827	2 retrocopies	retro_psin_14, retro_psin_43,