RetrogeneDB ID: retro_stub_153

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 9:8883602..8884097(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400016487
• Aliases: None
• Description: None

Sequence

>retro_stub_153
ACCAATTGGTGGTACGATATCAACAAGTCCATTCAATGGCAACATGGAATTTTCTTCACTCTTTGTGCTTTGTATTCCTT
TGTTTCGATTATCGCGCTAATTCAAGTGATAAGGATCCATTTAAGGATACCTTTATATGGTTGGTCAACACAAAAAGTGT
TTCATATAATGATTTTTGTTGCAAATGGTGTTGGTGCAATCGTTTTTGGGTTACATAACAAATTTTTTATATTACATTCA
AACGTTCTTATGACTCGCGCGATTTTAGACCTACAAGGATTGTTTTTCTTTACAACATTTACACACCTTGTTTGGTTTTG
GGCTGATGTTTATTACAAAATTCGAAGTTTTCCTACGAATAAGCTCAAAATTTGGTATATTTCGATAAATTGTGCAATAT
ACTTGATTCTGGGTTGTATATGGATTTGTATCGCGATGAATGACAATGACGCAGTAGTACTAGTGAAATTGTTGTTCATT
AGAAAGATATTTGTA

Alignment

ORF - retro_stub_153 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.58 %
• Parental protein coverage: 56.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TNWWDHVNESVQWQDGIFYSLCASYALVSAVALIQLIRIDLRVPEYGWTTQKVFHLMNFVVNGVRAIVFG
          TNWW...N.S.QWQ.GIF..LCA.Y..VS..ALIQ.IRI.LR.P.YGW.TQKVFH.M.FV.NGV.AIVFG
Retrocopy TNWWYDINKSIQWQHGIFFTLCALYSFVSIIALIQVIRIHLRIPLYGWSTQKVFHIMIFVANGVGAIVFG

Parental  FHKQVFLFHYKVL-TLAILDLPGLLFFSTFTLLVLFWAEIYHQARSLPTDKLRISYIATNGAIYFIQACI
          .H...F..H..VL.T.AILDL.GL.FF.TFT.LV.FWA..Y...RS.PT.KL.I.YI..N.AIY.I..CI
Retrocopy LHNKFFILHSNVLMTRAILDLQGLFFFTTFTHLVWFWADVYYKIRSFPTNKLKIWYISINCAIYLILGCI

Parental  WVYLWVNDNSTVEFIGKIFMAVVSV
          W.....NDN..V......F.....V
Retrocopy WICIAMNDNDAVVLVKLLFIRKIFV

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_153 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400016487	2 retrocopies	retro_stub_153 , retro_stub_92,