RetrogeneDB ID: retro_eeur_631

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_371214:80638..82486(+)
• 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_631
ATGCTTCTGCTCTGCCTTTTCCTCGGAATTCCGTGGAACACCCAAGCTCAGCAGATCCGGTACTCCGTTCCTGAGGAGTT
ACAGAAAGGCTCGTTTGTGGGCAATATTTCCAAAGACCTGGGTTTGGAGCCCCAGCAGCTGGCGGGGCACGGAGTCCGCA
TCGTCTCCCGAGGTAGGACGCAGCTCTTTGCTTTGCACCCGCGCAGCGGCAGCTTGGTCACCGCGGGCAGGATCGACCGC
GAGGAGCTCTGCGCTCAGAGCGCGCGGTGCCTGGTGAGTTTTAACATTCTTGTGGAAGACAGGGTCAAACTTTTCGGGGT
GGAAATAGAAGTGACCGATATCAATGATAATGCCCCCAAATTCCAAGCAAAAAATATAGATGTAAAAATTAATGAAAACG
TCGCTCCTGGAATGCGTTATCCTCTCCCGGAAGCGGTAGACCCGGATGTGGGCGTGAATTCCCTACAGAGCTACCAGCTC
AGCCCCAATGGCCACTTTTCGCTGGCAGTTCAAAGTCGTGCCAATGGGGTCAAGTACCCAGAGCTTGTGCTGGAGCACCC
ACTGGATCGGGAGGAAGAGGCCCTGCATCACCTGGTCCTCACTGCCTCTGATGGGGGTGACCCTCTCCGATCTGGCACCG
TCCACATCAGTGTGACTGTCTTCGATGCGAATGACAATGCCCCTGTTTTCTCCTTGCCTGAATACCGAGTGAGTGTCCCT
GAGAACCTGCCTGTGGGCACACAGCTGCTGACAGTCACTGCTACTGACCGAGATGAAGGGGCCAATGGAAAAGTGACGTA
TTCTTTCCGGAAAATATCTGATACGCAAACGTTGCAATTCCAACTAAACAAAGATACTGGGGAATTAAAAATATCAGAAA
ACCTAGATTATGAAGAAGCAGGTTTCTATGAATTAGAAATACAAGCAGAAGATGGAGGAGCTTATCTTGCAACGGCAAAA
GTACTGATTACAGTAAAAGATGTAAATGACAACAGTCCAGAAGTGACCGTCACATCTCTTTTTAGTCCCCTGATGGAAGG
TTCACCTGTGGGGACAGTTGTAGCCCTTTTAAATGTGCATGATCTAGACTCTGGGCAGAATGGACAAGTCACCTGTTCCA
TATTGGGGGATTTACCATTTAAATTAGAAAAGTCTATTGATGGTTACTATAGGTTAGTGACCCAAAGAGCCCTTGACAGG
GAACAGACTTCCTCTTATAATATCACCATAATGGCTACAGATGGAGGAAACCCATCACTGTCAACAGAAACTCACTTCAC
TCTACAAGTGGCAGATATCAATGACAACCCACCCACCTTTTCTCACATCTCCTACTTTACCTATATCCCAGAGAACAACC
CCAGAGGTTCCTCCATCTTCTCTGTGACCGCTTTAGACCCAGACAGCAAAGAAAATGCTCAGGTTATTTACTCATTAGTG
GAAGATACCATTCAAGGTATACCTCTGTCATCCTACATCTCCATCAACTCTGACACAGGAGTCCTTTATGCTCTTCGATC
CTTTGACTATGAGCAGTTCCGTGATCTGCAGATGTGGGTGATTGCCACCGACAGTGGGAACCCACCTCTCAGCAGCAATG
TTTCGCTGAACTTGTTCATACTGGACCAGAATGACAATGTTCCTGAGATCTTGTACCCCACCCTCCCCACTGATGGTTCC
ACAGGAGTGGAGCTGGCACCCCGCTCTGCAGAGCCCGGATACCTGGTGACCAAGGTGGTGGCAGTGGACAGAGACTCAGG
CCAGAATGCCTGGCTGTCCTACCGCCTGCTCAAGGCCAGTGAGCCAGGGCTCTTCTCAGTGGGGCTGCACACAGGTGACG
TGCACACC

Alignment

ORF - retro_eeur_631 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.81 %
• Parental protein coverage: 75.12 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVQLCLFVGLLLEVQAGKILYFVPEETVKGFFVGSIAKDLGLQAQELAGRGIRIVSRGRTQLFALNPRSG
          ...LCLF.G.....QA..I.Y.VPEE..KG.FVG.I.KDLGL..Q.LAG.G.RIVSRGRTQLFAL.PRSG
Retrocopy MLLLCLFLGIPWNTQAQQIRYSVPEELQKGSFVGNISKDLGLEPQQLAGHGVRIVSRGRTQLFALHPRSG

Parental  SLVTAGRIDREELCAQSARCLVSFNILVEDKMKLFPIEVEILDINDNAPHFQIEELELKMNEITSPGTRI
          SLVTAGRIDREELCAQSARCLVSFNILVED..KLF..E.E..DINDNAP.FQ......K.NE...PG.R.
Retrocopy SLVTAGRIDREELCAQSARCLVSFNILVEDRVKLFGVEIEVTDINDNAPKFQAKNIDVKINENVAPGMRY

Parental  PLPFGQDFDVGVNSLQSYQLSSNPHFFLDVQQGADGLQHPEMVLQSPLDREQEAVHHLVLTASDGGDPVR
          PLP...D.DVGVNSLQSYQLS.N.HF.L.VQ..A.G...PE.VL..PLDRE.EA.HHLVLTASDGGDP.R
Retrocopy PLPEAVDPDVGVNSLQSYQLSPNGHFSLAVQSRANGVKYPELVLEHPLDREEEALHHLVLTASDGGDPLR

Parental  SGMLRIHVQVVDANVNPPTFTQAQYQVSVLENVPLGTQLLTVKATDPDEGANGEVTYAFHNIDHRVAQIF
          SG...I.V.V.DAN.N.P.F....Y.VSV.EN.P.GTQLLTV.ATD.DEGANG.VTY.F..I.......F
Retrocopy SGTVHISVTVFDANDNAPVFSLPEYRVSVPENLPVGTQLLTVTATDRDEGANGKVTYSFRKISDTQTLQF

Parental  QLDPHMGEITNKEPLDFEEYNLYPMEIQAQDGAGLMARAKVLVKVLDINDNAPEVTITSVTASVPENFPP
          QL....GE....E.LD.EE...Y..EIQA.DG....A.AKVL..V.D.NDN.PEVT.TS......E..P.
Retrocopy QLNKDTGELKISENLDYEEAGFYELEIQAEDGGAYLATAKVLITVKDVNDNSPEVTVTSLFSPLMEGSPV

Parental  GTIIALINVHDQDSGDNGHTTCSISRNLPFKLEKLVDNYYRLVTEKTLDRELTPTYNITVTATDQGTPAL
          GT..AL.NVHD.DSG.NG..TCSI...LPFKLEK..D.YYRLVT...LDRE.T..YNIT..ATD.G.P.L
Retrocopy GTVVALLNVHDLDSGQNGQVTCSILGDLPFKLEKSIDGYYRLVTQRALDREQTSSYNITIMATDGGNPSL

Parental  STEAHISLHITDINDNSPVFSQDSYSAYIPENNPRGASIFSVTAHDADSNENAQVNYFLAEDDILGAPLS
          STE.H..L...DINDN.P.FS..SY..YIPENNPRG.SIFSVTA.D.DS.ENAQV.Y.L.ED.I.G.PLS
Retrocopy STETHFTLQVADINDNPPTFSHISYFTYIPENNPRGSSIFSVTALDPDSKENAQVIYSLVEDTIQGIPLS

Parental  SYVSINSDIGVLYALCSFDYEQFRELQLWVTALDSGKPPLSSNVSLRLFILDQNDNVPEILYPTLPTDGS
          SY.SINSD.GVLYAL.SFDYEQFR.LQ.WV.A.DSG.PPLSSNVSL.LFILDQNDNVPEILYPTLPTDGS
Retrocopy SYISINSDTGVLYALRSFDYEQFRDLQMWVIATDSGNPPLSSNVSLNLFILDQNDNVPEILYPTLPTDGS

Parental  TGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGEVHT
          TGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTG.VHT
Retrocopy TGVELAPRSAEPGYLVTKVVAVDRDSGQNAWLSYRLLKASEPGLFSVGLHTGDVHT

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	5.32 RPM	6.77 RPM
SRP017611_kidney	0.94 RPM	0.75 RPM
SRP017611_liver	0.48 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_631 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,