RetrogeneDB ID: retro_eeur_637

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_372563:3805..6136(+)
• 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_637
CTGATCCTGCTGTGCGCCTTCCTGGCCACAATGTGGGAGGTCGGAAGGGGACAGCTCCACTACTCGGTGCCTGAAGAGAG
TGACAAAGGGTCATTTGTAGGTAATATATCCAAGGACCTGGGACTAGAGTCACCAGAGCCAGTGAAGCACGGAGTCCGCA
TCGTTTCCCGAGGAAGGACGCAGCTTTTTGCTTTGAACGCCCGCGGTGGCAGTTTGGTCACAGCAGGCAGGATCGACCGC
GAAGAGCTCTGCGCTCAGAGCGCGCGGTGTCTTATAAATATCAACATCCTGGTTGAGGATAAAGGGAGACTTTTTGGAAT
AGAAATAGAAATTATTGATATCAATGACAATAACCCCAAGTTCCAAGTGGAACACCAGGAGGTGAAAATTAATGAGATCG
CTGCGCCCGGAACTCGTTATCCACTCCCAGAGGCTGTTGACCCGGATGTGGGCGTGAATTCCCTACAGAGCTACCAGCTC
AGCCCCAACGACCATTTCTCCCTGGATGTGCAAACTGGAGACGACGGAACTAGGAACCCAGAGCTGGTGCTGGAGCGCGC
CCTGGACCGGGAGGAAAGGGTTGTTCATCACTTGGTGCTCACCGCCTCGGATGGCGGTGACCCGCGTCGCTCCAGCACGA
TGCACATCCAAGTGACAGTGCTGGATACGAACGACAATGCCCCTGTTTTTGCGCAACAGATTTACCGCGTGAAAGTCCCA
GAAGACTTGCCCCCTGGCACCCTGCTGCTGACTGTCAGAGCCAGCGACCCAGATGAAGGAAGCAATGGAGAAGTGACATA
TAAATTCTGGAAAATCAGTGAAAAACAATCTCCGTTATTCCAGCTTAATGAAGACACTGGGGAAATAGCAATAGCAAAGA
GTCTAGATTATGAAGAATGTGCTTTTTATGAAATGGAAATACAAGCTGAAGATGTGGGGGCACTACTGGGGCGGACCAAA
GTGTTCATTTCAGTAGAAGATGTAAATGACAATAGGCCGGAAGTGATTATTACATCTCTGTTTAACCCAGTTTTGGAAAA
TACTCTGCCGGGCACAGTAATTGCCTTCTTGAATGTGCATGACCGAGACTCTGGGAAGAATGGTCAAATCATCTGTCACA
CACGTGAAAATATACCTTTTCAGTTAGAAAAATCAATTGATAATTATTATAGATTAGTAACATGGAAATATTTGGATAGA
GAAAAGACCTCTATGTACAATATTACAGTGATAGCCTCAGATCTAGGAATTCCACCTCTGTCTACTGAAACATATATTGC
TGTGCATGTGGCAGATACCAATGACAATCCACCCACTTTCACTCAGTCCTCCTACTCGGCTTATGTCCCTGAGAATAATC
TCAGAGGTGTTTCGATCTTCTCTATGACTGCCTATGACCCTGACAGTGGCAACAATGCAGTGGTCACTTACTCTGTAGTG
GAGAACACCATCATGGATGCACCACTCTCCTCTACTATCTCTATCAACTCTGACACTGGTGTGTTGTATGCTCTGTGCTC
ATTTGACTATGAACAGATTCAAGACGTGCAGTTATTGGTGATAGCTAGTGACAATGGGGACCCACCACTCAGTAGTAATG
TGTCCCTGAGGCTGTTCATTCTGGACCAGAATGACAACATACCAGAGATCCTCTACCCCATTCTTCCTACTGATGGTTCC
ACTGGGGTGGAGCTGGCACCCCGCTATGCAGAGCCCGGATACCTGGTGACCAAGGTGGTGGCAGTGGACAGAGACTCAGG
CCAGAATGCCTGGCTGTCCTACCGCCTGCTCAAGGCCAGTGAGCCAGGGCTCTTCTCAGTGGGGCTGCACACAGGTGAAG
TGCACACTGCCAGGGCCCTGCTGGACAGAGATGCTCTCAAGCAGAGCCTAGTGGTGGCAGTGCAGGACCATGGCCAGCCC
CCTCTCTCAGCCACTGTCACACTCACTGTGGCCATAGCTGACAGCATCCCAGATGTGCTGGCTGACCTGGGCAGCCTGGA
GTCTCCTGCCAGTCCTGAAGATTCTGACCTCACACTCTACCTGGTGGTGGCACTAGCCTCTGTGTCCTGCATCTTCCTTG
CCTTTGTCATCGTGCTGCTGGCTGTCAGGCTGAGGCGCTGGCACACATCCCACCTGCTCCAGGCTTCAGCAGGTGGACTG
GCTGGCCTTCCTGCCTCTCACTTTATGGGTGTGGATGGGGTGCAGGCTTTCCTGCAGACCTATTCCCATGAAGTGTCCCT
CACTGCAGACTCCAGGAAGAGTCACCTGATCTTCCCCCAGCCCAACTATGCTGACACCCTCATCAGCCAGGAGAGCTGTG
AGAAAAGTGAG

Alignment

ORF - retro_eeur_637 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.59 %
• Parental protein coverage: 94.76 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVQLCLFVGLLLEVQAGKILYFVPEETVKGFFVGSIAKDLGLQAQELAGRGIRIVSRGRTQLFALNPRSG
          L..LC.F.....EV..G...Y.VPEE..KG.FVG.I.KDLGL...E....G.RIVSRGRTQLFALN.R.G
Retrocopy LILLCAFLATMWEVGRGQLHYSVPEESDKGSFVGNISKDLGLESPEPVKHGVRIVSRGRTQLFALNARGG

Parental  SLVTAGRIDREELCAQSARCLVSFNILVEDKMKLFPIEVEILDINDNAPHFQIEELELKMNEITSPGTRI
          SLVTAGRIDREELCAQSARCL...NILVEDK..LF.IE.EI.DINDN.P.FQ.E..E.K.NEI..PGTR.
Retrocopy SLVTAGRIDREELCAQSARCLININILVEDKGRLFGIEIEIIDINDNNPKFQVEHQEVKINEIAAPGTRY

Parental  PLPFGQDFDVGVNSLQSYQLSSNPHFFLDVQQGADGLQHPEMVLQSPLDREQEAVHHLVLTASDGGDPVR
          PLP...D.DVGVNSLQSYQLS.N.HF.LDVQ.G.DG...PE.VL...LDRE...VHHLVLTASDGGDP.R
Retrocopy PLPEAVDPDVGVNSLQSYQLSPNDHFSLDVQTGDDGTRNPELVLERALDREERVVHHLVLTASDGGDPRR

Parental  SGMLRIHVQVVDANVNPPTFTQAQYQVSVLENVPLGTQLLTVKATDPDEGANGEVTYAFHNIDHRVAQIF
          S....I.V.V.D.N.N.P.F.Q..Y.V.V.E..P.GT.LLTV.A.DPDEG.NGEVTY.F..I.......F
Retrocopy SSTMHIQVTVLDTNDNAPVFAQQIYRVKVPEDLPPGTLLLTVRASDPDEGSNGEVTYKFWKISEKQSPLF

Parental  QLDPHMGEITNKEPLDFEEYNLYPMEIQAQDGAGLMARAKVLVKVLDINDNAPEVTITSVTASVPENFPP
          QL....GEI.....LD.EE...Y.MEIQA.D...L..R.KV...V.D.NDN.PEV.ITS....V.EN..P
Retrocopy QLNEDTGEIAIAKSLDYEECAFYEMEIQAEDVGALLGRTKVFISVEDVNDNRPEVIITSLFNPVLENTLP

Parental  GTIIALINVHDQDSGDNGHTTCSISRNLPFKLEKLVDNYYRLVTEKTLDRELTPTYNITVTATDQGTPAL
          GT.IA..NVHD.DSG.NG...C....N.PF.LEK..DNYYRLVT.K.LDRE.T..YNITV.A.D.G.P.L
Retrocopy GTVIAFLNVHDRDSGKNGQIICHTRENIPFQLEKSIDNYYRLVTWKYLDREKTSMYNITVIASDLGIPPL

Parental  STEAHISLHITDINDNSPVFSQDSYSAYIPENNPRGASIFSVTAHDADSNENAQVNYFLAEDDILGAPLS
          STE..I..H..D.NDN.P.F.Q.SYSAY.PENN.RG.SIFS.TA.D.DS..NA.V.Y...E..I..APLS
Retrocopy STETYIAVHVADTNDNPPTFTQSSYSAYVPENNLRGVSIFSMTAYDPDSGNNAVVTYSVVENTIMDAPLS

Parental  SYVSINSDIGVLYALCSFDYEQFRELQLWVTALDSGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDGS
          S..SINSD.GVLYALCSFDYEQ....QL.V.A.D.G.PPLSSNVSLRLFILDQNDN.PEILYP.LPTDGS
Retrocopy STISINSDTGVLYALCSFDYEQIQDVQLLVIASDNGDPPLSSNVSLRLFILDQNDNIPEILYPILPTDGS

Parental  TGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL
          TGVELAPR.AEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL
Retrocopy TGVELAPRYAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHTARALLDRDALKQSL

Parental  VVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPGDSDLTLYLVVAVAVVSCVFLAFVIVLL
          VVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASP.DSDLTLYLVVA.A.VSC.FLAFVIVLL
Retrocopy VVAVQDHGQPPLSATVTLTVAIADSIPDVLADLGSLESPASPEDSDLTLYLVVALASVSCIFLAFVIVLL

Parental  AVRLRRWHTSRLLQASAGELAGLPASHFVGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ
          AVRLRRWHTS.LLQASAG.LAGLPASHF.GVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ
Retrocopy AVRLRRWHTSHLLQASAGGLAGLPASHFMGVDGVQAFLQTYSHEVSLTADSRKSHLIFPQPNYADTLISQ

Parental  ESCEKRE
          ESCEK.E
Retrocopy ESCEKSE

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	6.61 RPM	6.77 RPM
SRP017611_kidney	1.13 RPM	0.75 RPM
SRP017611_liver	0.00 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_637 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,