RetrogeneDB ID: retro_stub_59

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 12:58972575..58973445(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400016876
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400004872
• Aliases: None
• Description: None

Sequence

>retro_stub_59
ATGACTATCCAACTAGAGGGAAAAAAAATCCAAGACCAAGACCAATTCATGGTGCCTCAAACAAATGCATTTGGACATAA
TTTTAGGGACTACAACAATGCACAAAGTGAAAGGCAAAAAGGGGTAGAAAAATTCTACAAAACACAACATATAAATCAAA
CATATGATTTTGTGAAGAAAATGAGAGAAGATTATACAAAATTAGACAAAGCAAAAATGAGCATATGGGAATGTTGTGAA
TTACTAAATGATGTTGTTGATGATAGTGATCCTGATTTAGATGAACCACAAATTCAACATTTATTACAGAGTGCTGAGGC
AATTAGAAAAGATTATCCTAATGAAGATTGGTTACATTTAACAGCCTTAATTCATGATTTAGGCAAAATATTAGTTTTAC
CTAAGTTTGGTGGTTTACCTCAATGGGCTGTTGTTGGTGACACATTCCCTTTAGGATGTTCATTTGATGAATCAAATATT
CACCATAAATATTTTAAAGAAAATCAAGATTTTAACAACTCAATTTACAACACAAAAAATGGAATATATAATGATTTTAT
TGGACTAGAAAATGTCATGATGTCATGGGGTCATGATGATTATATGTATATGGTTGCTAAAGAAAATGGTACAACATTAC
CATCAGCTGGACTTTTTATTATAAGGTATCATTCATTTTATCCATTGCATAAAAATGGAGCTTATAAACATTTGATGAAT
GATGAAGATGAAGAAAATTTGAAGTGGCTTCATGTTTTTAATAAATATGATTTGTATAGTAAAAGCAAAGTTCATGTTAA
TGTGGAAGAGGTAAAACCTTATTATATGTCTTTAATTGAGAAATATTTTCCAGCAAAGCTAAGGTGGTGA

Alignment

ORF - retro_stub_59 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.52 %
• Parental protein coverage: 91.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGFAVPQTNAFGHNFRDYT-VESARQQGVEFFYKINHFNQTYDYVSKMRVDYAKLDKAEMSIWECCELLN
          D.F.VPQTNAFGHNFRDY....S.RQ.GVE.FYK..H.NQTYD.V.KMR.DY.KLDKA.MSIWECCELLN
Retrocopy DQFMVPQTNAFGHNFRDYNNAQSERQKGVEKFYKTQHINQTYDFVKKMREDYTKLDKAKMSIWECCELLN

Parental  DVVDDSDPDLDEPQIQHLLQSAEAIRKDYPNEDWLHLTALIHDLGKVLLLPSFGELPQWAVVGDTFPVGC
          DVVDDSDPDLDEPQIQHLLQSAEAIRKDYPNEDWLHLTALIHDLGK.L.LP.FG.LPQWAVVGDTFP.GC
Retrocopy DVVDDSDPDLDEPQIQHLLQSAEAIRKDYPNEDWLHLTALIHDLGKILVLPKFGGLPQWAVVGDTFPLGC

Parental  AFHDSIVHSKYFKENPDYNNPAYNSKFGVYSEGCGLDKVLMSWGHDDYMYLVAKENGTTLPSAGLFIIRY
          .F..S..H.KYFKEN.D.NN..YN.K.G.Y....GL..V.MSWGHDDYMY.VAKENGTTLPSAGLFIIRY
Retrocopy SFDESNIHHKYFKENQDFNNSIYNTKNGIYNDFIGLENVMMSWGHDDYMYMVAKENGTTLPSAGLFIIRY

Parental  HSFYALHKSGAYKELMNEEDKENLKWLHIFNKYDLYSKSKVQVNVEEVKPYYMSLIEKYFPAKLKW
          HSFY.LHK.GAYK.LMN.ED.ENLKWLH.FNKYDLYSKSKV.VNVEEVKPYYMSLIEKYFPAKL.W
Retrocopy HSFYPLHKNGAYKHLMNDEDEENLKWLHVFNKYDLYSKSKVHVNVEEVKPYYMSLIEKYFPAKLRW

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_59 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400004872	1 retrocopy	retro_stub_59 ,
Solanum lycopersicum	Solyc06g062430.2	1 retrocopy	retro_slyc_5,