RetrogeneDB ID: retro_stub_123

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 5:31664300..31664561(-)
• Located in intron of: PGSC0003DMG400033659

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_123
TTAACTTCAGCTTATGTTAGAGACATGGTTATGCCCACTGTCAACAAGGGTAAGCCAGAGCTTACAAAGAAGGTTATGCC
TGCTGTTATTGTTCGCAAGCCATGGCATAGAAAGGGCGTTGTTAACATGTACCTTGAAGATAATGTTGTGGTGATTATGA
GTCCAAAGGGTGAAATGGAAGGGTCTGCAATCACTTCCCCAATTGGGAAAGAGTGCTGATCTTTGACCTAGGATCGCTAG
TGTGCTGCCAATGCTACTGTT

Alignment

ORF - retro_stub_123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.54 %
• Parental protein coverage: 63.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPSACVGDMVMATVKKGKPELRKKVMPAVIVRQRKPWRRKDGVFMYFEDNAGVIVNPKGEMKGSAITGPI
          L.SA.V.DMVM.TV.KGKPEL.KKVMPAVIVR..KPW.RK..V.MY.EDN..VI..PKGEM.GSAIT.PI
Retrocopy LTSAYVRDMVMPTVNKGKPELTKKVMPAVIVR--KPWHRKGVVNMYLEDNVVVIMSPKGEMEGSAITSPI

Parental  GKECADLWPRIASAANAIV
          GKEC..L......AANA.V
Retrocopy GKEC*SLT*DR*CAANATV

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_123 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,