RetrogeneDB ID: retro_stub_134

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 6:55489234..55489794(-)
• Located in intron of: PGSC0003DMG400007163

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400015434
• Aliases: None
• Description: None

Sequence

>retro_stub_134
ATGGTTGAGCTCAAGTTTCTTGGATTGGATTTGGTTATGTTGTGGGAACCCATAGCAAAGGTGAATTCCTGGAAAAGGAT
TGTTTGCTTCCATTAATATCCAAGCTCCTTGGTTATGCTATTGTTACTGCCTCCACCACTGTTAAACTTCCTCAGAAATT
GAAAATGCTCCAATGCTGAAGTGTTAGTGTTGTGAGCATTGAGCTTGAAGTAGTTGGTTATACCATTGCTTAAGCATAGT
CTTCACAAAGGACTTCCATTTTGTGCTTTTGGAGAGAATGCTTTTCTTTTGACTCAAGCTATCATTCTGGTTGCGATCAT
CTATTATTTTTCTCTGCCTTTGGGAGCGAAGACATGGATTAGAGCATTATCATATTGTGCTATAGCCCCATCTGTTTTGG
CAGATCAAATTGATCCCATCCTTTTTGATGCCTCATATGCCTATCAGCACGCAACTTTCTTTTTGCTAGTATGCCCAGAT
CTGGAAGAGTTTTAAGAACAGAAGTACTGGGGAGCTAAGCTGTTTAACCTTTTTTAATGAACTTTGGTGGTTCCATGTTA

Alignment

ORF - retro_stub_134 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.5 %
• Parental protein coverage: 80.25 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MVELKFLGMD-FGCALGSLSNGQFPEKDCLLPLISKLLGYAIVAASTTVKLPQILKILQHKSVRGLSVVA
          MVELKFLG.D.FG...G..S.G.F.EKDCLLPLISKLLGYAIV.ASTTVKLPQ.LK.LQ..SV...SVV.
Retrocopy MVELKFLGLD<FGYVVGTHSKGEFLEKDCLLPLISKLLGYAIVTASTTVKLPQKLKMLQC*SV---SVVS

Parental  FELELLGYTIA-LAYCLHKGLPFSAFGEYLF-LLIQAIILVAIIYYFSQPLGMKTWMKGLLYCAVAPTIL
          .ELE..GYTIA.L.....K...F......LF.LL.QAIILVAIIYYFS.PLG.KTW...L.YCA.AP..L
Retrocopy IELEVVGYTIA<LSIVFTKDFHFVLLERMLF<LLTQAIILVAIIYYFSLPLGAKTWIRALSYCAIAPSVL

Parental  AGQIDPVLFEALYASQHAI-FLCARIP-QIWKNFKSKSTGELSFLTFF-MNFAGSMV
          A.QIDP.LF.A.YA.QHA..FL.A..P.QIWK.FK..STGELS.LTFF.MNF.GSM.
Retrocopy ADQIDPILFDASYAYQHAT<FLFASMP<QIWKSFKNRSTGELSCLTFF>MNFGGSML

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_134 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	PGSC0003DMG400015434	1 retrocopy	retro_stub_134 ,
Solanum lycopersicum	Solyc12g088660.1	1 retrocopy	retro_slyc_88,