RetrogeneDB ID: retro_stub_87

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:11094291..11094657(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400017151
• Aliases: None
• Description: None

Sequence

>retro_stub_87
CGTCCGGGATGTCGAAACGAGGAAGATGAGGTTTCGTCGGGTCTGTCGGTGGCGGCGACGGTGAACTGCGCCGATAGCAC
TGGTGCTAAGAACCTGTACATCATTTCCGTGAAAGGGATCAAGGGAAGGCTTAACAGGTTGCCTTCAGCTTGTGTTGGAG
ATATGGTAATGGCTACTGTAAAGAAGGGTAAGCCATATCTCAAGAAGAAGGTTATGCTTGCTGTCATTGTTCGTCAGCGC
AAGCCATGGCGCCGAAAGGACGGTGTCTTCATGTACTTTGAAGATAATGCTGGTGTGATTGCGAACCCCAAGGGAGAAAT
GAAAGGGTTTGCGATGACTGGCCCAATTGGTAAAGAATGAATTGAT

Alignment

ORF - retro_stub_87 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.61 %
• Parental protein coverage: 87.14 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGGSAGNKFRMSLGLPVAATVNCADNTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPELRKK
          R.G........S.GL.VAATVNCAD.TGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKP.L.KK
Retrocopy RPGCRNEEDEVSSGLSVAATVNCADSTGAKNLYIISVKGIKGRLNRLPSACVGDMVMATVKKGKPYLKKK

Parental  VMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPIGKECAD
          VM.AVIVRQRKPWRRKDGVFMYFEDNAGVI.NPKGEMKG.A.TGPIGKE..D
Retrocopy VMLAVIVRQRKPWRRKDGVFMYFEDNAGVIANPKGEMKGFAMTGPIGKE*ID

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_87 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_7g098290	1 retrocopy	retro_mtru_54,
Solanum tuberosum	PGSC0003DMG400017151	2 retrocopies	retro_stub_123, retro_stub_87 ,
Solanum lycopersicum	Solyc09g090610.2	1 retrocopy	retro_slyc_83,