RetrogeneDB ID: retro_eeur_140

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_8727:9688..12100(+)
• 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_140
CTGGTCCTGCTGTGCGCGCTCCTGGGGACGTTGTGCATGATGGGATCCGGGCAGGTCCGCTACTCTGTGCCTGAGGAGCT
GGACAAAGGTTCCTTCGTGGGCAACATCGCCGAGGACTTAGGGCTGGAACCGCAGCAGCTGGCAGGACGCGGAGTCCGCA
TCATCTCCCGAGGTAGGACGCAGCTCTTCGTTTTGCACCCGCGCAGCGGCAGCTTGGTCACCGCAGACAGGATCGACCGC
GAGGAGCTCTGCGCTCAGAGCGCGCAGTGTCTGGTCAAATTTAACATCCTGGTGGAAGACAAGTTGAAAATCTTTGAAGT
AGAAGTAGAAGTCACAGATATTAACGATAATGCTCCTGACTTCCTGACACAGGATATGGAAATAAAAATTGGGGAACTAA
CAACTCCTGGCACGCGCTTTCCGCTTAAGACTGCCTTTGACCCAGACGTGGGCATCAACTCCCTGCAGAGCTACCAGCTA
AGTCATAGCGACTTCTTCTCCCTGGCGATGAAGAGCGTCTCTGATGGAACCAAGTACCCACAGTTGGTGCTGGAGCGAGC
TCTGGACCGCGAGGACAAAGAACTTCACCAGGTTGTTCTGGTGGCTTCTGATGCAGGTGAACCTGTTCATTCTGGCAACC
TGTACATCCAAGTGGTAGTTCTGGATGCAAATGACAACCCGCCTGTGTTTACTCAGCCAGAGTATCGAGTAAGTGTTCAG
GAGAAGTTGCCAGTGGGCACCAGGCTGCTCACTGTCAATGCCACTGACCCTGATGAGGGCTTCAATGCTCAGGTATCCTA
TGTACTAGACAAGATGCCTGGGAAAATTGCTCAGATGTTTTCTCTCAATTCGGTAACTGGAGATATATCATTACTAAGAA
ATCTGGACTATGAGGATGCTATGTTCCATGAAATTAAAATTGAAGCAGTAGATGGACCAGGACTCCTTTCAGAAGCTAAG
ATTCTAGTCACAGTTCTGGATGTGAATGACAATGCCCCAGAAGTTACAATCACTTCTCTCACAGGGTCAGTCCCAGAAGA
AACTACTCCTGGAAGAGAAGTTGCCCTTATACATGTGCATGACCGAGACTCCGGACAAAATGGACAAGTCACAGTTTCTG
TCCTGGGAAACATGCCTTTTAATTTAGAAAAATCAATAGGCCAGTATTACCGCTTGGTGACAGCCAGATCCCTGGACCGA
GAACAAGTTCCCAAATATAACATCACACTGAGAGCCACAGATGGAGGAATTCCACCACAGACCACAGACACTCACATCTC
CCTGCAGGTGACAGACACCAATGACAACCCACCTGCCTTCACACATGCCTCCTACTCTGCCTTCATTCAGGAAAACAACC
CCAGGGGGGCTTCCATCTTCTGTGTGACTGCCCAGGACCCTGACAGCACTGAGAATGCCCAAGTCACCTATGCTCTGACT
GAGGAGACTGTCCAAGGGTCACCTCTCTCCACTTATGTCTCCATCAACTCTGACACCGGAGTCTTGTATGCACTGCACTC
CTTTGATTATGAACAGGTTAGAGACCTGCAGCTACAGGTGACAGCCTGTGACAATGGGAAGCCTCCACTCAGCAGCAATG
TGTCCCTGAGGCTTTTCATTCTGGACCAGAATGACAATGTTCCTGAGATCTTGTACCCCACCCTCCCCACTGATGGTTCC
ACAGGAGTGGAGCTGGCACCCCGCTCTGCAGAGCCTGGATACCTGGTGACCAAGGTGGTGGCAGTGGACAGAGACTCAGG
CCAGAATGCCTGGCTGTCCTACCGCCTGCTCAAGGCCAGTGAGCCAGGGCTCTTCTCAGTGGGGCTGCACACAGGTGAGG
TGCACACTGCCAGGGCCCTGCTGGACAGAGATGCTCTCAAGCAGAGCCTGGTGGTGGCAGTGCAGGACCATGGCCAGCCC
CCTCTCTCAGCCACTGTCACACTCACTGTGGCCATAGCTGACAGCATCCCAGATGTGCTGGCTGACCTGGGCAGCCTGGA
GTCTCCTGCCAGTCCTGGAGATTCTGACCTCACACTCTACCTGGTGGTGGCAGTGGCCGTGGTCTCCTGTGTCTTCCTTG
CCTTTGTCATCGTGCTGCTGGCTGTCAGGCTGAGGCGCTGGCACACATCCCGCCTGCTCCAGGCTTCAGCAGGTGAACTG
GCTGGCCTTCCTGCCTCTCACTTTGTGGGTGTGGATGGGGTGCAGGCTTTCCTGCAGACCTATTCCCATGAGGTGTCCCT
CACTGCAGACTCCAGGAAGAGTCACCTGATCTTCCCCCAGCCCAACTATGCTGACACCCTCATCAGCCAGGAGAGCTGTG
AGAAAAGTGAGCCTCTTCTGGTACCTCAAGATTTTCTTGAAGCAAAAGGTGAAACCAAGCTACCCCAAGTAAGTTATATC
TTTCTTTGAAAA

Alignment

ORF - retro_eeur_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.77 %
• Parental protein coverage: 98.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVQLCLFVGLLLEVQAGKILYFVPEETVKGFFVGSIAKDLGLQAQELAGRGIRIVSRGRTQLFALNPRSG
          LV.LC...G.L.....G...Y.VPEE..KG.FVG.IA.DLGL..Q.LAGRG.RI.SRGRTQLF.L.PRSG
Retrocopy LVLLCALLGTLCMMGSGQVRYSVPEELDKGSFVGNIAEDLGLEPQQLAGRGVRIISRGRTQLFVLHPRSG

Parental  SLVTAGRIDREELCAQSARCLVSFNILVEDKMKLFPIEVEILDINDNAPHFQIEELELKMNEITSPGTRI
          SLVTA.RIDREELCAQSA.CLV.FNILVEDK.K.F..EVE..DINDNAP.F.....E.K..E.T.PGTR.
Retrocopy SLVTADRIDREELCAQSAQCLVKFNILVEDKLKIFEVEVEVTDINDNAPDFLTQDMEIKIGELTTPGTRF

Parental  PLPFGQDFDVGVNSLQSYQLSSNPHFFLDVQQGADGLQHPEMVLQSPLDREQEAVHHLVLTASDGGDPVR
          PL....D.DVG.NSLQSYQLS....F.L......DG...P..VL...LDRE....H..VL.ASD.G.PV.
Retrocopy PLKTAFDPDVGINSLQSYQLSHSDFFSLAMKSVSDGTKYPQLVLERALDREDKELHQVVLVASDAGEPVH

Parental  SGMLRIHVQVVDANVNPPTFTQAQYQVSVLENVPLGTQLLTVKATDPDEGANGEVTYAFHNIDHRVAQIF
          SG.L.I.V.V.DAN.NPP.FTQ..Y.VSV.E..P.GT.LLTV.ATDPDEG.N..V.Y.........AQ.F
Retrocopy SGNLYIQVVVLDANDNPPVFTQPEYRVSVQEKLPVGTRLLTVNATDPDEGFNAQVSYVLDKMPGKIAQMF

Parental  QLDPHMGEITNKEPLDFEEYNLYPMEIQAQDGAGLMARAKVLVKVLDINDNAPEVTITSVTASVPENFPP
          .L....G.I.....LD.E........I.A.DG.GL...AK.LV.VLD.NDNAPEVTITS.T.SVPE...P
Retrocopy SLNSVTGDISLLRNLDYEDAMFHEIKIEAVDGPGLLSEAKILVTVLDVNDNAPEVTITSLTGSVPEETTP

Parental  GTIIALINVHDQDSGDNGHTTCSISRNLPFKLEKLVDNYYRLVTEKTLDRELTPTYNITVTATDQGTPAL
          G...ALI.VHD.DSG.NG..T.S...N.PF.LEK....YYRLVT...LDRE..P.YNIT..ATD.G.P..
Retrocopy GREVALIHVHDRDSGQNGQVTVSVLGNMPFNLEKSIGQYYRLVTARSLDREQVPKYNITLRATDGGIPPQ

Parental  STEAHISLHITDINDNSPVFSQDSYSAYIPENNPRGASIFSVTAHDADSNENAQVNYFLAEDDILGAPLS
          .T..HISL..TD.NDN.P.F...SYSA.I.ENNPRGASIF.VTA.D.DS.ENAQV.Y.L.E....G.PLS
Retrocopy TTDTHISLQVTDTNDNPPAFTHASYSAFIQENNPRGASIFCVTAQDPDSTENAQVTYALTEETVQGSPLS

Parental  SYVSINSDIGVLYALCSFDYEQFRELQLWVTALDSGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDGS
          .YVSINSD.GVLYAL.SFDYEQ.R.LQL.VTA.D.GKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDGS
Retrocopy TYVSINSDTGVLYALHSFDYEQVRDLQLQVTACDNGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDGS

Parental  TGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL
          TGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL
Retrocopy TGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL

Parental  VVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPGDSDLTLYLVVAVAVVSCVFLAFVIVLL
          VVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPGDSDLTLYLVVAVAVVSCVFLAFVIVLL
Retrocopy VVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPGDSDLTLYLVVAVAVVSCVFLAFVIVLL

Parental  AVRLRRWHTSRLLQASAGELAGLPASHFVGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ
          AVRLRRWHTSRLLQASAGELAGLPASHFVGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ
Retrocopy AVRLRRWHTSRLLQASAGELAGLPASHFVGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ

Parental  ESCEKREFLSAPQSSLEDSKETFSQVNFYTYLNK
          ESCEK.E.L..PQ..LE...ET......Y..L.K
Retrocopy ESCEKSEPLLVPQDFLEAKGETKLPQVSYIFL*K

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	25.46 RPM	6.77 RPM
SRP017611_kidney	5.25 RPM	0.75 RPM
SRP017611_liver	1.45 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_140 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,