RetrogeneDB ID: retro_stub_37

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 8:53483311..53484382(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400003916
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG401027186
• Aliases: None
• Description: None

Sequence

>retro_stub_37
ATGGTGGAGGCACAGTCATGGACTACAAGAAGGGGCAGCAATCCAAGATTGGAGTCACCCCAAGATCAAGTCTTGGATAT
GCCAGTAACCCCAACTGCTGAAATCAGGCAGCAACAGTATTCTAATGGTGGGATAACTTCTTTGGTGTCACCAAATGTAC
TTACTGCTCTTATAATTGCTTCTTGGTACTGTTCAAATATTGGGGTGTTGTTGCTAAACAAGTATCTTTTAAGTTTTTAT
GGTTATCGTTACCCAATATTCTTGACTATGTTGCATATGTTGTCATGTGCTACTTATAGTTTAGTTGCTATTAAGTGGCT
GGAAGTTGTTCCTTTCCAGCAGATACATAGCAGGAAACAGTTCTTCAATATTCTTGCTTTGAGTGCTATTTTTTGTTTTT
CTGTTGTGTGTGGTAATACTTCATTGAGGTACCTTCCTGTATCGTTTAATCAAGCAATTGGTGCTACTACCCCATTTTTT
ACTGCTATTTTTGCTTTTGTGATTACTTGTAAGAAAGAAACTGCTGAGGTTTATTTAGCTCTTGTCCCTGTGGTTCTTGG
TATTGTTTTGGCTAGCAATAGTGAGCCATTGTTCCATTTGTTTGGGTTCTTGATGGCTTTAGGTTCAACTGCTGGGAGAG
CCTTGAAATCTGTTGTTCAGGGGTTGTTGTTATCCTCTGATGCTGAGAAATTACACTCCATGAATCTGTTATTATACATG
GCTCCAATGGCAGCAATGATTTTGCTTCCTTTTACACTATACATAGAGGGGAATGTAGCAGCAGTTACAGTGGAGAAAGC
TAAGGGAGATAGATTTATGGTTTTCTTGTTGATTGGTAATGCCACAGTTGCTTATTTGGTGAACTTAACTAATTTCTTGG
TTACTAAGCATACAAGTGCCTTGACACTGCAAGTTTTGGGGAATGCCAAGGCTGCAGTGGCTGCAGTGGTGTCAGTTTTG
ATATTCAGGAATCCAGTGAACATCATGGGCATAACAGGATTTGCTGTGACTGTAATGGGTGTGGTGCTTTACAGTGAGGC
AAAGAAGAGATCTAAAGTAACAGCACACTGA

Alignment

ORF - retro_stub_37 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.69 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SGQFFTIGLVTAWYSSNIGVLLLNKYLLSNYGFKYPIFLTMCHMTACSLLSYIAIAWMKIVPMQTIRSRV
          S....T......WY.SNIGVLLLNKYLLS.YG..YPIFLTM.HM..C...S..AI.W...VP.Q.I.SR.
Retrocopy SPNVLTALIIASWYCSNIGVLLLNKYLLSFYGYRYPIFLTMLHMLSCATYSLVAIKWLEVVPFQQIHSRK

Parental  QFMKISALSLIFCTSVVSGNISLRYLPVSFNQAIGATTPFFTAVFAYLMTFKREAWLTYVTLIPVVTGVV
          QF..I.ALS.IFC.SVV.GN.SLRYLPVSFNQAIGATTPFFTA.FA...T.K.E....Y..L.PVV.G.V
Retrocopy QFFNILALSAIFCFSVVCGNTSLRYLPVSFNQAIGATTPFFTAIFAFVITCKKETAEVYLALVPVVLGIV

Parental  IASGGEPSFHLFGFIICIGATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPIAVVFLLPATLMMEENV
          .AS..EP.FHLFGF....G.TA.RALKSV.QG.LLSS..EKL.SMNLLLYMAP.A...LLP.TL..E.NV
Retrocopy LASNSEPLFHLFGFLMALGSTAGRALKSVVQGLLLSSDAEKLHSMNLLLYMAPMAAMILLPFTLYIEGNV

Parental  VGITLALARDDSRIIWLLLFNSALAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVISILIFRNPVSVT
          ...T...A..D.....LL..N...AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA.V.S.LIFRNPV...
Retrocopy AAVTVEKAKGDRFMVFLLIGNATVAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAAVVSVLIFRNPVNIM

Parental  GMLGYALTVFGVILYSEAKKRSK
          G..G.A.TV.GV.LYSEAKKRSK
Retrocopy GITGFAVTVMGVVLYSEAKKRSK

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_37 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6,
Medicago truncatula	MTR_3g070000	1 retrocopy	retro_mtru_1,
Solanum tuberosum	PGSC0003DMG401027186	1 retrocopy	retro_stub_37 ,
Prunus persica	PRUPE_ppa009115mg	1 retrocopy	retro_pper_41,
Solanum lycopersicum	Solyc05g052790.2	1 retrocopy	retro_slyc_35,
Theobroma cacao	TCM_042615	1 retrocopy	retro_tcac_6,