RetrogeneDB ID: retro_stub_23

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:55446624..55448625(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400028270
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400005011
• Aliases: None
• Description: None

Sequence

>retro_stub_23
ATGCGGGTGAAGAACAAAACCCCTGCCCCAATCCAAATCACGGCAGAGCAGATTTTCCGGGAAGCTAGAGAACGTCAAGA
GGCGGAAATCAGACTGCCCAAACAGAAAATCAGTGACCCAACAGAAGGAGCTGATTATCGCCTTCGCAAGCGAAAGGAAT
TTGAGGGTTTAATTAGCCGTGTAGGCTGGAACAAGAGTGTGTGGGTGAAATATGCTGAATGGGAAGAATCACAAAAGGAC
TTGAAGCGTGCTCGTTCTATATGGGAACGTGCACTTGGAGTTGATGCACTTAACCGTGACCATACCATCTGGTTGAAGTA
TGTTGATATGGAGATGAAGAATAAGTTTGTTAATCATGCTCGTAATCTATGGGATCGAGCTGTTATCCGTTTGCCTAGGG
TTGATCAGTTGTGGTACAAGTATATTCATATGGAAGAGATGCTTGGCAATGTAGCTGGTGCAAGACAGATTTTTGAGAGG
TGGATGAGGTGGATGCCGGACCAGCAAGGGTGGTTATCTTATATTAAGTTTGAGTTAAGGTATAATGAAATAGAGAGGGC
AAGAGAAATTTTTGAGAGATTTGTGGAGTGTCATCCGAAAGTTAGTGCTTGGATTAGGTTCTCAAAATTTGAGATGAAGA
ATGGGGAGATTGGGAGGGCAAGGAATTGTTATGAAAGGGCTGTGGATAAGTTGGGAGATGACGATGACGAAGCTGAGCAG
TTGTTTCTGGCATTCGCAGAGTTTGAGGACAAGTGTAAGGAGACGGACAGGGCACGTTGCATATATAAATTTGCCCTTGA
TCAGATACCAAAAGGGCGAGCTGAGGATTTGTACGGCAAGTTTGTGGCATTTGAAAAGCAGTATGGTGATAGGGAAGGTA
TTGAGGATGCTATAGTTGGAAAAAGGAGGTTTCAGTATGAGGATCAAGTCAAGATGAATCCACGTAACTATGATACATGG
TTTGATTATATTCGTCTAGAAGAGAGCATTGGAAATAAAGAGAGGATTAGAGAGGTTTATGAGAGAGCCATTGCTAATGT
TCCTCCTGCTGAAGAGAAGCGGTATTGGCAACGATACATTTACTTATGGATTAATTATGCATTATATGAAGAGATTGATG
CACAAGACATGGAAAGAACCAGACATGTTTACCTGGAGTGTCTTAAGCTGATTCCACATCACAAGTTTTCATTTGCAAAG
ATTTGGTTGTTGGCTGCCTTGTTTGAGATTCGGCAGTTAAGACTCAAGGAGGCACGGCTTCTACTTGGAGAAGCGATTGG
AAGGGCTCCTAAAGACAAGATATTTAATAAGTACATTGAGATAGAGCTGCAATTTGGGAACATAGATCGTTGCAGAAAGC
TTTATGAGAAGTACTTAGAATGGTCACCAGAAAATTGCCATGCTTGGAGCAAATTCGCCGGGTTAGAGAGGTCCTTGTAT
GAAACGGAGAGAGCCAGAGCTGTTTTTGAGCTTGCAATTGATCAACCTGCACTGGATATTCCAGAGTTACTATGGAAGGC
TTACATAGACTTCGAGATCTCTGAGGGTGAATTTGAAAGAACAAGAGCACTATATGAAAGACTTCTTAACCGTACCAAAC
ATTTAAAGGTGTGGATAAGTTATGCCAAGTTTGAGGCATCGGCTATGGAATCAGATGTTGAACAGAAAAAGAAGTGCCTG
CAAAATGCTAGAGATGTTTTTGAGAGGACCGTTTCTTACTTAAGAATATCTGCACCTGAACTGAAGGAAGAAAGAGGAAT
GCTTTTGGAAGAATGGCTAAATATGGAAAACAGTTTTGGTGAGCTTGGAGATGTCAATTTAGTCCATGCCAAACTACCAA
AGAAACTGACGAAGAGAAGGCAAATAGACATGGAGGATGGTCCAGCAGTCTACGAGGAGTACATAGACTATCTTTTCCCT
GAAGAAATGCAGGCGAACAATCTTAACATTTTGGCTTCTGCTTATAAATGGAAGAAACAGCGGGTTGCATCCGAGGATTA
G

Alignment

ORF - retro_stub_23 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.64 %
• Parental protein coverage: 96.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RVKNKTPAPIQITAEQILREARERQEAEIRPPKQKITDPTELADYRLRKRKEFEALISRVRWNKSVWVKY
          RVKNKTPAPIQITAEQI.REARERQEAEIR.PKQKI.DPTE.ADYRLRKRKEFE.LISRV.WNKSVWVKY
Retrocopy RVKNKTPAPIQITAEQIFREARERQEAEIRLPKQKISDPTEGADYRLRKRKEFEGLISRVGWNKSVWVKY

Parental  AKWEESQKDFKRARSIWERALEVDY--RDHTMWLKYADVEMKNKFVNHARNVWDRAVTLLPRVDQLWYKY
          A.WEESQKD.KRARSIWERAL.VD...RDHT.WLKY.D.EMKNKFVNHARN.WDRAV..LPRVDQLWYKY
Retrocopy AEWEESQKDLKRARSIWERALGVDALNRDHTIWLKYVDMEMKNKFVNHARNLWDRAVIRLPRVDQLWYKY

Parental  IHMEEMLGNVAGARQIFERWMGWMPDQQGWLSYIKFELRYNEIERARAIFERFVQCHPKVSAWIRFAKFE
          IHMEEMLGNVAGARQIFERWM.WMPDQQGWLSYIKFELRYNEIERAR.IFERFV.CHPKVSAWIRF.KFE
Retrocopy IHMEEMLGNVAGARQIFERWMRWMPDQQGWLSYIKFELRYNEIERAREIFERFVECHPKVSAWIRFSKFE

Parental  MKNGEIGRARNCYERAVDKLADDE-EAEQLFVAFAEFEEKCKEAERARCIYKFALDHIPKGRAEDLYRKF
          MKNGEIGRARNCYERAVDKL.DD..EAEQLF.AFAEFE.KCKE..RARCIYKFALD.IPKGRAEDLY.KF
Retrocopy MKNGEIGRARNCYERAVDKLGDDDDEAEQLFLAFAEFEDKCKETDRARCIYKFALDQIPKGRAEDLYGKF

Parental  VAFEKQYGDREGIEDAIVGKRRFQYEDEVRKNPRNYDTWFDYIRLEESVGNKERIREVYERAIANVPPAE
          VAFEKQYGDREGIEDAIVGKRRFQYED.V..NPRNYDTWFDYIRLEES.GNKERIREVYERAIANVPPAE
Retrocopy VAFEKQYGDREGIEDAIVGKRRFQYEDQVKMNPRNYDTWFDYIRLEESIGNKERIREVYERAIANVPPAE

Parental  EKRYWQRYIYLWINYALYEELDAEDMERTRDVYRECLKLIPHQKFSFAKIWLLAAQFEIRQLRLKEARLL
          EKRYWQRYIYLWINYALYEE.DA.DMERTR.VY.ECLKLIPH.KFSFAKIWLLAA.FEIRQLRLKEARLL
Retrocopy EKRYWQRYIYLWINYALYEEIDAQDMERTRHVYLECLKLIPHHKFSFAKIWLLAALFEIRQLRLKEARLL

Parental  LGEAIGRAPKDKIFKKYIEIELHFGNIDRCRKLYEKYLEWSPENCYAWSKFAELERSLYETDRARAIFEL
          LGEAIGRAPKDKIF.KYIEIEL.FGNIDRCRKLYEKYLEWSPENC.AWSKFA.LERSLYET.RARA.FEL
Retrocopy LGEAIGRAPKDKIFNKYIEIELQFGNIDRCRKLYEKYLEWSPENCHAWSKFAGLERSLYETERARAVFEL

Parental  AIDQPALDMPELLWKAYIDFEISEGEFERTRALYERLLNRTKHLKVWISYAKFEASAMDPEAEEDIELKK
          AIDQPALD.PELLWKAYIDFEISEGEFERTRALYERLLNRTKHLKVWISYAKFEASAM......D.E.KK
Retrocopy AIDQPALDIPELLWKAYIDFEISEGEFERTRALYERLLNRTKHLKVWISYAKFEASAME----SDVEQKK

Parental  NCLQRARDVFERAVSYFRNSAPELKEERAMLLEEWLNMESGFAELGDVSLVRAKLPKKLKKRRQIDMEDG
          .CLQ.ARDVFER.VSY.R.SAPELKEER.MLLEEWLNME..F.ELGDV.LV.AKLPKKL.KRRQIDMEDG
Retrocopy KCLQNARDVFERTVSYLRISAPELKEERGMLLEEWLNMENSFGELGDVNLVHAKLPKKLTKRRQIDMEDG

Parental  PAAYEEYIDYLFPEETQTTNLKILEAAYKWKKQRVASEE
          PA.YEEYIDYLFPEE.Q..NL.IL..AYKWKKQRVASE.
Retrocopy PAVYEEYIDYLFPEEMQANNLNILASAYKWKKQRVASED

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_23 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400005011	2 retrocopies	retro_stub_23 , retro_stub_36,
Triticum aestivum	Traes_7DL_41F6E8FC4	1 retrocopy	retro_taes_37,