RetrogeneDB ID: retro_stub_133

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 6:43312054..43312291(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400016534
• Aliases: None
• Description: None

Sequence

>retro_stub_133
ACACTACGTGTGAGATGTGGAAGACGGAGTTTCCATCTCCAAAAAGCCATCTTTCTGCTTGTGCTTACCCTGCTACACAT
AAAAGGACATACAACTGGAGTGTGAAGGCAACTCGCAAAAAGATAACTTGAATTGGCCAAATGAGGTATCTTAATTCGTA
ACGTCCCTCGCAGGTTCAAGATCAATTTCAGAGAATGTACTGAAGCAGCTCCAAATAAGAAGGCAGCAATTTCTGCT

Alignment

ORF - retro_stub_133 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.43 %
• Parental protein coverage: 82.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TLCVRCGRRSFHLQK-SRCSACAYPAARKRTYNWSVKAIRRKTTGTGRMRYLRN-VPRRFKTNF-REGTE
          TL.VRCGRRSFHLQK.S..SACAYPA..KRTYNWSVKA.R.K.T..G.MRYL....P......F.RE.TE
Retrocopy TLRVRCGRRSFHLQK<SHLSACAYPATHKRTYNWSVKATRKKIT*IGQMRYLNS*RPSQVQDQF>RECTE

Parental  AAPRKKGVASA
          AAP.KK...SA
Retrocopy AAPNKKAAISA

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_133 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400002541	1 retrocopy	retro_stub_124,
Solanum tuberosum	PGSC0003DMG400016534	1 retrocopy	retro_stub_133 ,