RetrogeneDB ID: retro_stub_2

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:46545917..46546814(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400010588
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400026715
• Aliases: None
• Description: None

Sequence

>retro_stub_2
ATGAGTGACGAAAGAAGAGTTCACCCAAATTGTGGGAATGGTTCGAACCCTTATCATGAATGCAGTGAATATTGCTTCAA
AATAATAGCGGCAATAAAGAAGCAAATGATCAAAGCTGAAACATGTGTGTTGCAAGCTAATACTGTTGATGTTCATCGCT
CCGATGCACCTGATGAAAGAGATGGTGTTGAAAGTCACAGTGATGATGGAGAGGATAATATGGGAGAAGAGTCGGTGAAT
CTGATAACAGGGAGGAAGAGGAAGTTATTTGAATTGAGGTTAAAAATGAATGTGGCAAGAAAAGCTAATCAATCTGCAAT
GGTAGTAGAGAAGAAAAAAACAGAAGCTCCCCCTGCAGAGTGTAGAGGAATGTCCAAGCAACAATGGATTGAAGAGAGGA
AGAAGAAAATCGGGAATTTGTTGGATGCCAAAGGGTTAGATATGAGCAAGGCATATATGCTAGATACACAAGAGTCTGCA
GAGACAAAGTATAAGAAATGGGAGAAGGAGCCTGCTCCAGCTGGTTGGGATGTTTTTAATAAGAAGACGCTATACAATGC
ATACAAGAAGCGGACAAAGAATGTTGATGTTGATGTAGATGAGTACAATAGAATGAAGGAAACTGTTCCAGAATTTTATC
GAGAAGCTTCAAGTCTCCAGTATGGAAAGGCACCAAAATTGTCAGACGAAAAGATAGAGAGGATGGTGAAGGAGCTAAAG
GACAGGGACGAGAAGCGCCAATCATTTAGTCGGAGGAGAAAGTTCCATGAAGAGAAAGACATTGACTCTATTAATGATCG
TAACGAGCATTTCAATAAAAAGATTGAGCGTGCCTTTGGAAAATACACCTTGGAGATCAAGAATAACCTTGAGAGAGGAT
CTGCTTTGCCTGATTGA

Alignment

ORF - retro_stub_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.87 %
• Parental protein coverage: 73.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DGEDNMGQDSANL-TGRKKKIFELRLKMNEARKANQSAMVAEKKKTEAPP-ESRGMSKQKWIEERKKKIG
          DGEDNMG..S.NL.TGRK.K.FELRLKMN.ARKANQSAMV.EKKKTEAPP.E.RGMSKQ.WIEERKKKIG
Retrocopy DGEDNMGEESVNLITGRKRKLFELRLKMNVARKANQSAMVVEKKKTEAPPAECRGMSKQQWIEERKKKIG

Parental  KLLDANGLDMSKAYMLDTQESAEVKYKKWEKEPAPAGWDVFNQKTLYDAYKKRTKNVAVDVDEYNRMKEA
          .LLDA.GLDMSKAYMLDTQESAE.KYKKWEKEPAPAGWDVFN.KTLY.AYKKRTKNV.VDVDEYNRMKE.
Retrocopy NLLDAKGLDMSKAYMLDTQESAETKYKKWEKEPAPAGWDVFNKKTLYNAYKKRTKNVDVDVDEYNRMKET

Parental  DPEFYREASSLQYGKAPKLSDDKIERMVKELKDRDEKRQSFSRRRKFHEEKDIDSINDRNEHFNKKIERA
          .PEFYREASSLQYGKAPKLSD.KIERMVKELKDRDEKRQSFSRRRKFHEEKDIDSINDRNEHFNKKIERA
Retrocopy VPEFYREASSLQYGKAPKLSDEKIERMVKELKDRDEKRQSFSRRRKFHEEKDIDSINDRNEHFNKKIERA

Parental  FGKYTLEIKNNLERGTALPD
          FGKYTLEIKNNLERG.ALPD
Retrocopy FGKYTLEIKNNLERGSALPD

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_2 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400026715	1 retrocopy	retro_stub_2 ,