RetrogeneDB ID: retro_stub_101

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 2:43169038..43170505(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400021536
• Aliases: None
• Description: None

Sequence

>retro_stub_101
TTGCATCTAATTGAAGATATGGAACTTGTTCTCACCTTAAGATGCCTCTGGAATATTGCTCTTGCTCAACCTGATGACCC
TGAATTCCCGTCCCTCGGCGTTTTTAATTGCATGGCTAGACTTCTCAACAGCTGCACCCGTGACCAAAAATGGCTTTCAA
GAGGTCATAACGTGTATGTCCCTTATTATGCAGCTCATATCATTGGCTCCTACACCATGAACAAAGCTAGATTCTCTGTT
TTGGCTGTTAAATCAGGCGTAATTTCGCCATTAATAGACCTCTTAAGAGGTAAGATAACTTGGGTCGAGCAAAGAGTGGC
TGTTAGAGCACTTGGTCACATTGCGCGACATAGAAGGACATTTGAAGACATTATGGTCCATGAAGTAGAGATTATGAAAC
TAGCCATGGACATAGCTTCCAAATGCATTTTTACAATCTATAGCGAGTTTGTGTGCAAGAAAACTGAAAACAGAGTCGAA
TATCATTGCTATTTGATGACAAAAGGTCTCAGAGAATTCGAAATGGAGAATAAAAAAGCAGAGTCTTGGGCTTGCCAAAT
GCAATGCTGGTCTCTATACCTTCTCAACTGCTTCATTACAAAGAAAAGAAGCATCAATTTAATATGCAAAGAAGATTTTC
TCAAGAATTTATGTGATATATGGGGTGGATTACAGAACCAGAATTCTTTCTCTGGCATTGGCCTAATCAGAAGTCTTTGT
GAAAGCGAAGATGGTAGAAAAAACATTGCTCAATTAGAACAAGTCGTAGAAAATATCTGCAACCTCTCTAGATCATCGGA
CGAATGGCAATTCATGGCAATTGAAAGTCTTTTGGTACTTCTCAAGGATCCAAAAACAAGAAACAGAGTAACCAACATTG
CAGCTCCTTTTCTTGCTGATTTAGTAGAGCTTAGAACTATCAAAGGAAGACGAAAAATCGGTGACATGATAACGCAACTA
CTCTTGCAAGATTATGCTAAAATCAAATATGGTCAAGTGGGGTTCGACGAAATAGGATCACAAAAGGCAATTGAAGAGAT
TTGGGACTTGAAAGTTGAAAAAAGGAAAAGGGATAAAATCATGTCGGAACAAGAAGTGAAGGAAACAGAGCTTTTGGTTT
CCGTTTTAAAACGTGAAGGAAACAAGAAATTTTGGTCAAGTGAGATTGAAGCAGCTGTAAACAAGTACACAAAGGCTTTA
GATTTATGTCCACTAAACTTAAGAAAAGAAAGGATTGTTCTTTATAGCAATAGAGCTCAATGTCATTTAATTTTAGGAGA
AGCAGAGTTAGCTATTAGTGATACAACTCGAGCCTTATGCTTATCAGGTGAAATGAGGCCACATATAAAGAGCCTGTGGC
GAAGATCGCAGGCTTATCACATGAAAGGATTGGCTAGACTAAGTTTAATGGATTGCTTAATGTTCATCAATGAACGAAGC
AAGTTGAATGGAAACAAAAGCAGCACA

Alignment

ORF - retro_stub_101 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.79 %
• Parental protein coverage: 82.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHLIDEDQELVLVLSGLWTMAMSQPNDKELPSLGIFECMASLINKGINQKSWLQKNQNIYIPYYASHIIG
          .HLI.ED.ELVL.L..LW..A..QP.D.E.PSLG.F.CMA.L.N.......WL....N.Y.PYYA.HIIG
Retrocopy LHLI-EDMELVLTLRCLWNIALAQPDDPEFPSLGVFNCMARLLNSCTRDQKWLSRGHNVYVPYYAAHIIG

Parental  SYTMNNVEFAIKALDCGVLVPLLDLLRGKMTWVEQRVAIRAIGHLASYEKTFKSVAIYEEEIVKLAMNLA
          SYTMN...F...A...GV..PL.DLLRGK.TWVEQRVA.RA.GH.A....TF......E.EI.KLAM..A
Retrocopy SYTMNKARFSVLAVKSGVISPLIDLLRGKITWVEQRVAVRALGHIARHRRTFEDIMVHEVEIMKLAMDIA

Parental  STCLEVVYKEFVGVKDLTMRLKYHCDLLTRGVGGLEMENSKAEEWASQLQCWSLHLLNCFAIKERCLNLI
          S.C....Y.EFV..K....R..YHC.L.T.G....EMEN.KAE.WA.Q.QCWSL.LLNCF..K.R..NLI
Retrocopy SKCIFTIYSEFV-CKKTENRVEYHCYLMTKGLREFEMENKKAESWACQMQCWSLYLLNCFITKKRSINLI

Parental  CEQIFLKELSEMWGGLANDSSPGGVGLIRVLCYNKDGRRCIAESKDVIKNLCNLARSSDDWQYMGIDCLL
          C...FLK.L...WGGL.N..S..G.GLIR.LC...DGR..IA....V..N.CNL.RSSD.WQ.M.I..LL
Retrocopy CKEDFLKNLCDIWGGLQNQNSFSGIGLIRSLCESEDGRKNIAQLEQVVENICNLSRSSDEWQFMAIESLL

Parental  LLLADSGTRYKVLKVASMCLVDLIELRTLGGRSNVGNTITRTLLADF---KQRKVKIKNIGVQQVLEEIW
          .LL.D..TR..V...A...L.DL.ELRT..GR...G..IT..LL.D....K...V....IG.Q...EEIW
Retrocopy VLLKDPKTRNRVTNIAAPFLADLVELRTIKGRRKIGDMITQLLLQDYAKIKYGQVGFDEIGSQKAIEEIW

Parental  GLKVDRKKREQNMSDEKLEEKRVMVSLMKQEGNNSFWLGKIEEAMMKYSEALELCPLRFRKERIVLYSNR
          .LKV...KR...MS.....E....VS..K.EGN..FW...IE.A..KY..AL.LCPL..RKERIVLYSNR
Retrocopy DLKVEKRKRDKIMSEQEVKETELLVSVLKREGNKKFWSSEIEAAVNKYTKALDLCPLNLRKERIVLYSNR

Parental  AQCKLLLGEANDAISDTTKALSLSSPTNSHSKSLWRRSQAYDMKGLAKESLVDCIMFVNCCFKMDYSSSS
          AQC.L.LGEA..AISDTT.AL.LS.....H.KSLWRRSQAY.MKGLA..SL.DC.MF.N...K.....SS
Retrocopy AQCHLILGEAELAISDTTRALCLSGEMRPHIKSLWRRSQAYHMKGLARLSLMDCLMFINERSKLNGNKSS

Parental  S
          .
Retrocopy T

Legend:

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

Expression

RNA-Seq

Solanum tuberosum was not studied using RNA-Seq expression data.

ChIP-Seq

Solanum tuberosum was not studied using ChIP-Seq data.

EST

Solanum tuberosum was not studied using EST data.

TSS

Solanum tuberosum was not studied using FANTOM5 data.

Lab

retro_stub_101 was not experimentally validated.

Homology

Retrocopy orthology:

Solanum tuberosum 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400021536	1 retrocopy	retro_stub_101 ,
Solanum lycopersicum	Solyc04g078170.1	1 retrocopy	retro_slyc_70,