RetrogeneDB ID: retro_stub_105

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 3:28377413..28377711(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400003291
• Aliases: None
• Description: None

Sequence

>retro_stub_105
ATTAGGATCACTCTTTCTACCAAAAACGTTAAGAATCTTGAGAAAATGTGTACCGATTTGGTCTGTGGTGCTTAGGACAG
GAGATTAGAGTAAAGGGACTTGTAGAAATGCCAACAAAGGTTCTTAACATTTTCCCTAGGAAGTCTTCCTATGGAGAAGG
CACGAATACGTGGGACAAGTTTGAGCTAGGGGTTCACGAGCGCTGATTGACCATTTTAGCTCCCCAAATGTTGTCAATCA
AATCACCTCAATCACCACTGTACTTGGTGTCGAGGTTGATGTCACCATGGTTGATTCC

Alignment

ORF - retro_stub_105 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 81.3 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IRITLSSKNVKNLEKVCADLVRGAKDKRL-RVKGPVRMPTKVLNITTRKSPCGEGTNTWDRFELRVHKR-
          IRITLS.KNVKNLEK.C.DLV.GA.D.RL.RVKG.V.MPTKVLNI..RKS..GEGTNTWD.FEL.VH.R.
Retrocopy IRITLSTKNVKNLEKMCTDLVCGA*DRRL<RVKGLVEMPTKVLNIFPRKSSYGEGTNTWDKFELGVHER<

Parental  VIDLFSSPDVVKQITSITIEPGVEVEVTIADS
          .ID.FSSP.VV.QITSIT...GVEV.VT..DS
Retrocopy LIDHFSSPNVVNQITSITTVLGVEVDVTMVDS

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_105 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400000965	3 retrocopies	retro_stub_104, retro_stub_108, retro_stub_65,
Solanum tuberosum	PGSC0003DMG400003291	1 retrocopy	retro_stub_105 ,
Physcomitrella patens	PP1S257_105V6	1 retrocopy	retro_ppat_38,