RetrogeneDB ID: retro_etel_284

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_4727:7921..9393(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCDHB15
• Ensembl ID: ENSETEG00000001310
• Aliases: None
• Description: protocadherin beta 15 [Source:HGNC Symbol;Acc:8686]

Sequence

>retro_etel_284
CGCTTTCCTAGATCAAGGCAAGTTCTGCTTCTCTTTGTTTGTCTGACTCAGACTTGCGCTGAGAGGGGAGGCTATATCGT
GGCGGAAGAAACGGAGAATGGTTCTTTTGTGGCAAATCTAGCAAAAGACTTAGGGCTAGGAATAAGAGAGTTGTCCTGGC
GGAGGGCTCGGGTTATTTCTGAGGACAACAAAAAACACTTTCAGCTGAACCTTCAGACTGGAGATTTGCAAGTCGCTGAG
AAGCTGGATAGGGAAGAACTGTGCGGCCCCATTGAGCTTTGTGAGCTGAAGCTCCAAATGTTGCTGGAAGACCCTTTGGA
GGCACACAGATTTAAACTGTGGGTTCTTGATATAAATGATAATGCCCCTATGTTTCCAGAAGCAGAAATGACGTTGAAAG
TCTTGGAAAATAGTCTTCCAGGGTCTGCGTTTCCCCTGCAGAATGCAAAAGATTTAGACATAGGCATAAATAATATTCAA
AACTACACCATCTACCCCAATTCCCATTTCCACATTCTCACCCGCCATGGAAGTGAGGGCAGGAAATACCCGGAGCTAGT
GCTAGACAAAGCCCTGGATCGTGAAGAGCAGCCAGAGCTGCGGGTAACTCTCACGGCAGTAGATGGTGGGGCTCCTCCCA
AGACCGGGACTGCCTTGGTCATCATTGATGTCTTAGATGTCAATGACAATGCCCCTGAGTTTGTGCAGTCACTCTATCAT
GTTCAGATACCTGAAGACAGCCCCCTCGGGTTCCTGATCGTCACTGTTTCTGCCAGAGATTTAGACACGGGAATCAATGG
TGAAATATTCTACTCATATTTTTATGGTGATGAAGAAATTGCCAAGACATTTGCACTTAATAAATTAACTGGAGAAATCA
AAATAATAAAGACCCTAGATTTTGAAAAGATTGCCTCATATGAAGTGACTATTAAGGCCTCTGATGGAGCAGGTCTTTCT
GGAAAGTGCACTGTGATTATACAGGTGGTGGATATAAACGACAACATGCCTGAACTAACTGTGGCTTCACTTATGAGCCG
CATCCCTGAAAATTCCGCAGAGACCAGAGTAGCTCTTTTTAGTATTCGAGACCGGGACTCAGGAGAAAATGGAAGAATGG
TTTGTTCTATCAAAGGAGACATTCCCTTCAGATTGAAACCAACCGTTGAAAATTTCTACACGCTGGTGACAGAGGGCACT
CTAGACAGAGAAAGCCAATCAGAGTACAATATCACCATTACAGTTTCTGATTTGGGGACCCCCAGGCTGAAAACCGAGCA
CACCATCAGGGTGCTGGTCTCCGACGTCAATGACAACGCGCCCACCTTCACCCAAACCTCCTACACGCTGTTCGTCCGCG
AGAACAACAGCCCCGGCGTGCACCTGGGCACAGTCAGCGCCACCGACAGAGACGCGGGCACCAACGCCCAAGTCATCTTA
CTCCCTGCTGCCGGCCTCGAGACCCGCACCTG

Alignment

ORF - retro_etel_284 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.59 %
• Parental protein coverage: 81.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RSPQQRQVLLLFLFLGVTLAGCEPRRYSVLEETGSGSFVANLANDLGLGVGELERRGARVVSEDSEPGLQ
          R.P..RQVLLLF..L..T.A..E...Y.V.EET..GSFVANLA.DLGLG..EL..R.ARV.SED.....Q
Retrocopy RFPRSRQVLLLFVCLTQTCA--ERGGYIVAEETENGSFVANLAKDLGLGIRELSWRRARVISEDNKKHFQ

Parental  LNTQTGELILNKKLDREELCGSAEPCVMPFQVVLKKPLEVFRAELLVRDINDHSPEFPEREMTLRIPESS
          LN.QTG.L....KLDREELCG..E.C....Q..L..PLE..R..L.V.DIND..P.FPE.EMTL...E.S
Retrocopy LNLQTGDLQVAEKLDREELCGPIELCELKLQMLLEDPLEAHRFKLWVLDINDNAPMFPEAEMTLKVLENS

Parental  PNGTVFPLKKAQDLDVGNNDVQKYTISPNSHFHVSTLKLGDGRKYPQLVLDKELDHEEQPEFRITITAQD
          ..G..FPL..A.DLD.G.N..Q.YTI.PNSHFH..T.....GRKYP.LVLDK.LD.EEQPE.R.T.TA.D
Retrocopy LPGSAFPLQNAKDLDIGINNIQNYTIYPNSHFHILTRHGSEGRKYPELVLDKALDREEQPELRVTLTAVD

Parental  GGSPPRFGTAQIRILVMDINDNAPEFSKTLYDVQVPENSPIGFLVAKVSARDLDTGINGDKSYSLFYNSP
          GG.PP..GTA...I.V.D.NDNAPEF...LY.VQ.PE.SP.GFL...VSARDLDTGING...YS.FY...
Retrocopy GGAPPKTGTALVIIDVLDVNDNAPEFVQSLYHVQIPEDSPLGFLIVTVSARDLDTGINGEIFYSYFYGDE

Parental  GIRKSFELSHLSGEIRLXXXXDFEAISSYDLHIEASDGGGLSGKCSVSIKVLDVNDNAPELTISSLTSPI
          .I.K.F.L..L.GEI......DFE.I.SY...I.ASDG.GLSGKC.V.I.V.D.NDN.PELT..SL.S.I
Retrocopy EIAKTFALNKLTGEIKIIKTLDFEKIASYEVTIKASDGAGLSGKCTVIIQVVDINDNMPELTVASLMSRI

Parental  PENSPDTEVALFRVRDRDSGDNGRIICSIQSDLPFLLKPSTENFYTLITDGALDREARAEYNVTITVTDL
          PENS..T.VALF..RDRDSG.NGR..CSI..D.PF.LKP..ENFYTL.T.G.LDRE...EYN.TITV.DL
Retrocopy PENSAETRVALFSIRDRDSGENGRMVCSIKGDIPFRLKPTVENFYTLVTEGTLDRESQSEYNITITVSDL

Parental  GSPRLKTEHTIRVLVSDVNDNAPTFTQTSYTLFVRENNSPGLHLGTVSATDRDAGTNAQV-TYSLLP-PR
          G.PRLKTEHTIRVLVSDVNDNAPTFTQTSYTLFVRENNSPG.HLGTVSATDRDAGTNAQV..YSLLP.PR
Retrocopy GTPRLKTEHTIRVLVSDVNDNAPTFTQTSYTLFVRENNSPGVHLGTVSATDRDAGTNAQV>SYSLLP>PR

Parental  DPHL
          DPHL
Retrocopy DPHL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_284 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001310	1 retrocopy	retro_etel_284 ,