RetrogeneDB ID: retro_stub_49

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 3:9607512..9608328(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG402022924
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400013285
• Aliases: None
• Description: None

Sequence

>retro_stub_49
ATGAGGCAAAACGATTCAGTTGAAGAGTTTGTTGATGTTGCAATTGAAGCAGCTAAGAAAGCTGGAGAGATAATTCGTCA
TGGATTCTACAAGAGTAAGCATGTTGAGCACAAAGGAGTTGTTGATTTAGTAACAGAGACTGATAAGGCATGTGAAGATT
TAATTTTTAATCATCTAAAGCAATGTTTTCCCAGTCATAAGTTTATTGGTGAAGAAACAACTGCTGCTGCTTCTGGAGAT
TTTGAGCTGACTGATGAACCAACTTGGATAGTTGATCCACTTGACGGAACCACCAACTTTGTGCACGGGTTTCCTTTTGT
TTGCGTATCTATCGGTCTCACAATTGAAAAGAAACCAGTAGTTGGTGTTGTTTACAACCCAATTATTGATGAGATTTTCA
CTGCAATCGATGGGAGAGGTGCTTTTCTTAACGGGAAGCCTATCAGAGTATCTTCAGAGTCTCAACTTGTAAAGGCTCTT
GTTGCTACAGAGGTTGGAACAAACAGGGATAAGGCAATTGTAGATGCTACTACAGGGAGAATCAATAGATTGCTTTTCAA
GGTTAGGTCCCTCAGGATGTCTGGTTCTTGTGCATTAAATCTATGTGGAGTGGCGTGTGGAAGGCTTGATCTCTTCTATG
AAATTGAATTTGGTGGTCCTTGGGATGTCGCAGCTGGTGCTCTCATAGTCACAGAAGCTGGAGGACTCGTGCTTGATCCA
TCTGGTTCCGAATTTGACCTAACAGCTCGACGGGTAGCTGCTACAAACGCTCATCTCAAGGACGCTTTTATCAACGCCTT
GAATGAATCAGAATGA

Alignment

ORF - retro_stub_49 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAQNGSVEEFLDVAVEAAKKAGEIIRQGFYKTKHVEHKGVVDLVTETDKACEDLIFDHLKQRFPSHKFIG
          M.QN.SVEEF.DVA.EAAKKAGEIIR.GFYK.KHVEHKGVVDLVTETDKACEDLIF.HLKQ.FPSHKFIG
Retrocopy MRQNDSVEEFVDVAIEAAKKAGEIIRHGFYKSKHVEHKGVVDLVTETDKACEDLIFNHLKQCFPSHKFIG

Parental  EETTASC-GNFELTDEPTWIVDPLDGTTNFVHGFPFVCVSIGLTIEKKPTVGVVYNPIIDELFTAIDGKG
          EETTA...G.FELTDEPTWIVDPLDGTTNFVHGFPFVCVSIGLTIEKKP.VGVVYNPIIDE.FTAIDG.G
Retrocopy EETTAAASGDFELTDEPTWIVDPLDGTTNFVHGFPFVCVSIGLTIEKKPVVGVVYNPIIDEIFTAIDGRG

Parental  AFLNGKPIKVSSQSELVKALLATEAGTNRDKLTVDATTGRINSLLFKVRSLRMCGSCALNLCGVACGRLD
          AFLNGKPI.VSS.S.LVKAL.ATE.GTNRDK..VDATTGRIN.LLFKVRSLRM.GSCALNLCGVACGRLD
Retrocopy AFLNGKPIRVSSESQLVKALVATEVGTNRDKAIVDATTGRINRLLFKVRSLRMSGSCALNLCGVACGRLD

Parental  LFYELEFGGPWDVAGGAVIVKEAGGFVFDPSGSEFDLTARRVAATNAHLKDAFIKALNE
          LFYE.EFGGPWDVA.GA.IV.EAGG.V.DPSGSEFDLTARRVAATNAHLKDAFI.ALNE
Retrocopy LFYEIEFGGPWDVAAGALIVTEAGGLVLDPSGSEFDLTARRVAATNAHLKDAFINALNE

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_49 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	PGSC0003DMG400013285	1 retrocopy	retro_stub_49 ,
Solanum lycopersicum	Solyc11g012410.1	1 retrocopy	retro_slyc_33,