RetrogeneDB ID: retro_stub_13

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 6:48397850..48398882(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400004895
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400031020
• Aliases: None
• Description: None

Sequence

>retro_stub_13
ATGGCAGAAGAAGTGAGCAACAAACAGGTCATTCTGAAACACTATGTCACCAGTTACCTTAAGGAATCAGACATGGAATT
AAAAAATACCACCATTAAATTGAATGTTCCAGAAGGTTCTAATGCGATGGTTTTGAAGAATCTTTTCTTGTCATGTGACC
CTTACATGCGTAACCGCATGAAGAAATTTGAGGGGGGCTATGTTGAGTCCTTCACTCCTGGCTCTCCTATCACGGGATAT
GGAGTGGCTAAAGTTTTGGAGTCTGGTGATTCGAACTTCCAGAAAGGTGACTTAGTTTTGGGAAGGACTGGATGGGAGGA
GTATAGTATTGTAACAGCTACTCCGACTCTGTTTAAAATTCGTGACAAGGATGTGCCTCTTTCCTACTATACAGGAATCC
TCGGTATGCCTGGTCTGACTGCTTATGCTGGTTTTTACGAGGTTTGCTCTCCTAAAAAGGGAGAAACTGTCTTTGTTTCA
GCTGCTTCCGGAGCAGTTGGTCAGCTTGTTGGGCAATTTGCAAAGATGTTGGGTTGCTATGTTGTTGGTAGTGCTGGAAG
TAAAGAAAAAGTTGATCGGTTGAAGAGCACATTTGGTTTTGATGAAGCTTTTAACTACAAAGAGGAGCAGGATTTGGACG
CGGCTTTGAAGAGGCACTTCCCTGATGGAATTGACATCTACTTTGAGAATGTTGGAGGGAAGATGCTTGATGCAGTTCTT
CTGAATATGAAAATCCATGGTCGTATTGCTGTGTGTGGGATGATCTCACAATACAACCTTGAGCAGACTGAAGGAGTGCA
CAACTTGTTCTGTCTCATCTCAAAACGAATCCGCATGGAAGGATTTCTTGTTTTTGATTACTATCATCTTTACCCTAAAT
ATTTGGAAATGATCATTCTGCAAATCAAAGCTGGTAAGGTTGTGTACGTGGAAGATGTAGCTGAAGGCCTCGAAAGTGCT
CCGAGTGCTCTAGTTGGTCTCTTCTCTGGTCGCAATATTGGAAAGCAAGTTGTGATGGTTTCGCGTGAATGA

Alignment

ORF - retro_stub_13 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.42 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGEEVSNKQIILKHHVTGNVKECDMELKKTTIKLNVPEGSNALLLKNLYLSCDPYMRSRMSKTEGSYIAP
          M.EEVSNKQ.ILKH.VT...KE.DMELK.TTIKLNVPEGSNA..LKNL.LSCDPYMR.RM.K.EG.Y...
Retrocopy MAEEVSNKQVILKHYVTSYLKESDMELKNTTIKLNVPEGSNAMVLKNLFLSCDPYMRNRMKKFEGGYVES

Parental  FTPDAPIMGIGVAKVLESGDSNFQKGDLVWGMTGWEEYSVVTTSQTFFKIHDKDVPLSYYTGILGMPGMT
          FTP..PI.G.GVAKVLESGDSNFQKGDLV.G.TGWEEYS.VT...T.FKI.DKDVPLSYYTGILGMPG.T
Retrocopy FTPGSPITGYGVAKVLESGDSNFQKGDLVLGRTGWEEYSIVTATPTLFKIRDKDVPLSYYTGILGMPGLT

Parental  AYAGFYEVCSPKKGETVFVSAASGAVGQLVGQFAKMMGCYVVGSAGSKEKVDLLKSKFGFDEAFNYKEEH
          AYAGFYEVCSPKKGETVFVSAASGAVGQLVGQFAKM.GCYVVGSAGSKEKVD.LKS.FGFDEAFNYKEE.
Retrocopy AYAGFYEVCSPKKGETVFVSAASGAVGQLVGQFAKMLGCYVVGSAGSKEKVDRLKSTFGFDEAFNYKEEQ

Parental  NLDATLKRYFPDGIDIYFENVGGKMLDAVLVNMKVHGRISACGMISQYNLEQTEGVHNLFCLITKQIRME
          .LDA.LKR.FPDGIDIYFENVGGKMLDAVL.NMK.HGRI..CGMISQYNLEQTEGVHNLFCLI.K.IRME
Retrocopy DLDAALKRHFPDGIDIYFENVGGKMLDAVLLNMKIHGRIAVCGMISQYNLEQTEGVHNLFCLISKRIRME

Parental  GFVVTDYYHLYPKYLEMIIPQIKAGKIVYVEDVAEGLESAPSALVGLFSGRNVGKQVVMVSTE
          GF.V.DYYHLYPKYLEMII.QIKAGK.VYVEDVAEGLESAPSALVGLFSGRN.GKQVVMVS.E
Retrocopy GFLVFDYYHLYPKYLEMIILQIKAGKVVYVEDVAEGLESAPSALVGLFSGRNIGKQVVMVSRE

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_13 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400031020	1 retrocopy	retro_stub_13 ,