RetrogeneDB ID: retro_stub_139

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:23697548..23698408(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400025528
• Aliases: None
• Description: None

Sequence

>retro_stub_139
ATGGGAGGAAGTTCAGTCAGTGATGATTGAGAGTTTATTGAAAATGAAACTCAGACAATACTTATGATTGGGTGTATAGG
TGAAGGAAAAAGTCCCACAGACAATAGCTTTCTTGGTAGAAAGCATTCAAGTTGAGGTCTAGCTCTGGTGGTGTTACAAG
AACTTGTGAGATTCAGAGGACTCAATTAGAAGATGGGTAGATTCTTGATGTGATCAATATCCCTGAATTTGATTTTAATG
CTGAATCTGGATTAGTTGTAAATGAAATTGGTAAATGCATTGATTTGGCCGATGATGGTGTCCACACAGTTCTTTTTATT
TTGTCTGTACGCACTAGCTTTTCATAAGAAGAACAGGCTGCTATACATTACTTTAAGAAGCTCTTTGGGACCAAAATTAG
TGATTACATGATTGTGGTCTACACTAGAGGGGATAAGCTCGAAGATAATGATTCTTTGAATAATCACTTAGATTGTTCCT
GCCGTGAGGATTTAAAGGAAGTTCTTAAGATGTGTGGGTATAGACAAGTGCTTTTCGACAATAAAACTTAAGATCCAGCA
AATAAAGCTGAACAATAGAGGGAACTTCTTTTCCATGTGAATCTGGTTGTACAAACGACTGGTGGAAAACCATATGCGAG
TGAATTATTTGAGGAAGTAAAGAAGATGAAGCTCTGTAATGACTCATTGGAGGTTAGTTCTTTTCTCGGAGATTTAAAGC
AAAGGGTAGCTGATGAGTTGAAGGAACAAGTGCAGAGGTTCTCTTTCAAGGAGCAATACAGGCGAATAACCGAAATGGTT
GAATCAAAGATTAACAATACCATGCATAGTCTTGAAAAGCAATTGGAGGAGCGTACTGCT

Alignment

ORF - retro_stub_139 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.16 %
• Parental protein coverage: 85.5 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGGSAISDDWEFTTTGARTLVLVGCTGNGKSATGNSIVGRK-AFKSMSSSAGVTSTCELQRTVLEDNQIL
          MGGS..SDD.EF......T....GC.G.GKS.T.NS..GRK.AFK..SSS.GVT.TCE.QRT.LED..IL
Retrocopy MGGSSVSDD*EFIENETQTILMIGCIGEGKSPTDNSFLGRK<AFKLRSSSGGVTRTCEIQRTQLEDG*IL

Parental  DVIDTPGLFDCSSEPEFVGNEIVKCINMAKDGIHAVLVVLSVRSRFSREEHAAVQSLREFFGSKISDYMI
          DVI..P..FD...E...V.NEI.KCI..A.DG.H.VL..LSVR..FS.EE.AA.......FG.KISDYMI
Retrocopy DVINIPE-FDFNAESGLVVNEIGKCIDLADDGVHTVLFILSVRTSFS*EEQAAIHYFKKLFGTKISDYMI

Parental  LVFTGGDDLEDNDETLDDYLGRDCPELLKNTLKMCGNRQVLFDNKTKDPLKKAEQLKQLLFLVNVVVENN
          .V.T.GD.LEDND..L...L...C.E.LK..LKMCG.RQVLFDNKT.DP..KAEQ...LLF.VN.VV...
Retrocopy VVYTRGDKLEDND-SLNNHLDCSCREDLKEVLKMCGYRQVLFDNKT*DPANKAEQ*RELLFHVNLVVQTT

Parental  AGKPYTDDLFKELKKGATKLHNQATEVNFLVGYTKQERL-ELKEQMQK-SYEEQLKRITEVVESKLKETT
          .GKPY...LF.E.KK...KL.N...EV....G..KQ....ELKEQ.Q..S..EQ..RITE.VESK...T.
Retrocopy GGKPYASELFEEVKK--MKLCNDSLEVSSFLGDLKQRVADELKEQVQRFSFKEQYRRITEMVESKINNTM

Parental  HRLEEQLAKEQA
          H.LE.QL....A
Retrocopy HSLEKQLEERTA

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_139 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 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400025528	2 retrocopies	retro_stub_139 , retro_stub_144,