RetrogeneDB ID: retro_stub_36

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 3:49680614..49682465(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400009506
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_stub_36
ATGGCTTCGGGTTACCTCACTCGTAAGGAAACGGAGGTAAAGGTTGCTATGGCTAGGCGGGTGAAGAACAAAACCCCAGC
CCCAATCCAAATCACGGCGGAGCAAATCCTCCGAGAAGCTAGGGAGCGTCAAGAGGCAGAAATCAGACCGCCCAACCAGA
AAATCACTGACCAAACAGAAGTAGCTGATTACCGTCTTCGCAAGCGAAAGGAATTTGAATCCTTAATTAGCCGTGTAGGC
TGGAACAAGAATGTGTGGGTGAAATATGCTGAATGGGAAGAATCACAAAACGACTTGAAGCGTGCTCGTTCTATCTGGGA
ACGTGCGCTTGGAATTGATGCACTTAACCGTGACCATACCATCTGGTTGAAGTATGTCCATATGGAGATGAAGAATAAGT
TTGTTAATCATGCTCGCAATCTATGGGATCGAGCTGTTATCCGTTTGCCTAGGGTTGATCAGTTGTGGTACAGGTATATT
CATATGGAAGAGATGCTCGGCAATGTAACTGGTGCAAGAGGGATTTTTGAGAGGTGGATGGGGTGGATGCCGGACCAGCA
AGGGTGGTTGTCTTACATTAAGTTTGAGTTAAGGTATAATGAAATAGAGAGGGCAAGAGAAATTTTTGAGAGATTGGTTC
AGTGTCATCCGAAAGTTATTGCTTGGATTAGGTTTGCAAAATTTGAGATGAAGAATGGGGAGATAGGGAGGGTAAGGAAT
TGTTATGAGAGGGCTGTGGATAAGTTGGCAGATGACGATGAGGAAGCTGAGCAGTTGTTTGTGGCATTTGCAGAATTCGA
GGAAAAGTGTAGGGAGACGGACAGAGCAAGGTGCATATATAAATTTGCACTTGATCACATACCGAAAGGGCGAGCTGAGG
ATTTGTTCAGCAAGTTTGTGGCATTTGAAAAGCAGTATGGTGATAGGGAAGGTATTGAGGATGTTATAGTTGGAAAAATG
AGGTTTCAATATGAGGATCAAGTAAAGAAGAATCCACGTAACTATGATACGTGGTTTGATTATATCCGTCTAGAAGAGCG
CATTGGAAATAAAGAGAGGATTAGAGAGGTTTATGAGAGAGCCATTGCTAATGTTCCTCCTGCTGAAGAGAAGCGGTATT
GGCAGCGATACATTTACTTATGGATTAATTATGCATTATATGAAGAGCTTGATGCACAAGATATGGAAAGGGCCAAACAT
GTTTACAGGGAGTGTCTTAAGCTGATTCCGCATCACAAGTTCTCATTTGCAAAGATTTGGTTGTTGGCTGCCCAGTTTGA
GATTCGGCAGTTAAGACTCAAGGAGGCACGACTTTTTCTTGGAGAAGCTATTGGTAGGGCTCCTAAAGACAAGATATTTA
AGAAGTACATTGAAATAGAGCTGCATTTGGGGAATATAGATCGTTGCAGAAAGCTTTATGAGAAGTACTTAGAATGGTCA
CCTGAAAACTGCTATGCTTGGAGCAAATTCGCTGAGTTAGAGAGGTCCTTGTATGAAACAGAGAGAGCCAGAGCTGTTTT
TGAGCTTGCAATTGACCAACCTGCACTGGATATTCCAGAGTTACTATGGAAGGCTTACATCGACTTTGAGATCTCTGAGG
GTGAATTTGAAAGAACAAGAGCACTATATGAAAGACTTCTTAACCGCACGAAACATTTAAATATGGAAAACACTTTCGGT
GAGCTACCAAAGAAACTGAAGAAGAGAAGGCAAATAGACATGGAGGATGGTCCAGCAGTCTACGAGGAGTACATAGACTA
TCTTTTCCCTGAAGAAATGCAGGCGAACAATCTTAACATTTTGGCTTCTGCTTATAAATGGAAGAAGCAGCGGGTTGCAT
CCAAGGATTAG

Alignment

ORF - retro_stub_36 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.67 %
• Parental protein coverage: 79.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYLTRKETEVKLPRPTRVKNKTPAPIQITAEQILREARERQEAEIRPPKQKITDPTELADYRLRKRKEFE
          GYLTRKETEVK.....RVKNKTPAPIQITAEQILREARERQEAEIRPP.QKITD.TE.ADYRLRKRKEFE
Retrocopy GYLTRKETEVKVAMARRVKNKTPAPIQITAEQILREARERQEAEIRPPNQKITDQTEVADYRLRKRKEFE

Parental  ALISRVRWNKSVWVKYAKWEESQKDFKRARSIWERALEVDY--RDHTMWLKYADVEMKNKFVNHARNVWD
          .LISRV.WNK.VWVKYA.WEESQ.D.KRARSIWERAL..D...RDHT.WLKY...EMKNKFVNHARN.WD
Retrocopy SLISRVGWNKNVWVKYAEWEESQNDLKRARSIWERALGIDALNRDHTIWLKYVHMEMKNKFVNHARNLWD

Parental  RAVTLLPRVDQLWYKYIHMEEMLGNVAGARQIFERWMGWMPDQQGWLSYIKFELRYNEIERARAIFERFV
          RAV..LPRVDQLWY.YIHMEEMLGNV.GAR.IFERWMGWMPDQQGWLSYIKFELRYNEIERAR.IFER.V
Retrocopy RAVIRLPRVDQLWYRYIHMEEMLGNVTGARGIFERWMGWMPDQQGWLSYIKFELRYNEIERAREIFERLV

Parental  QCHPKVSAWIRFAKFEMKNGEIGRARNCYERAVDKLADD-EEAEQLFVAFAEFEEKCKEAERARCIYKFA
          QCHPKV.AWIRFAKFEMKNGEIGR.RNCYERAVDKLADD.EEAEQLFVAFAEFEEKC.E..RARCIYKFA
Retrocopy QCHPKVIAWIRFAKFEMKNGEIGRVRNCYERAVDKLADDDEEAEQLFVAFAEFEEKCRETDRARCIYKFA

Parental  LDHIPKGRAEDLYRKFVAFEKQYGDREGIEDAIVGKRRFQYEDEVRKNPRNYDTWFDYIRLEESVGNKER
          LDHIPKGRAEDL..KFVAFEKQYGDREGIED.IVGK.RFQYED.V.KNPRNYDTWFDYIRLEE..GNKER
Retrocopy LDHIPKGRAEDLFSKFVAFEKQYGDREGIEDVIVGKMRFQYEDQVKKNPRNYDTWFDYIRLEERIGNKER

Parental  IREVYERAIANVPPAEEKRYWQRYIYLWINYALYEELDAEDMERTRDVYRECLKLIPHQKFSFAKIWLLA
          IREVYERAIANVPPAEEKRYWQRYIYLWINYALYEELDA.DMER...VYRECLKLIPH.KFSFAKIWLLA
Retrocopy IREVYERAIANVPPAEEKRYWQRYIYLWINYALYEELDAQDMERAKHVYRECLKLIPHHKFSFAKIWLLA

Parental  AQFEIRQLRLKEARLLLGEAIGRAPKDKIFKKYIEIELHFGNIDRCRKLYEKYLEWSPENCYAWSKFAEL
          AQFEIRQLRLKEARL.LGEAIGRAPKDKIFKKYIEIELH.GNIDRCRKLYEKYLEWSPENCYAWSKFAEL
Retrocopy AQFEIRQLRLKEARLFLGEAIGRAPKDKIFKKYIEIELHLGNIDRCRKLYEKYLEWSPENCYAWSKFAEL

Parental  ERSLYETDRARAIFELAIDQPALDMPELLWKAYIDFEISEGEFERTRALYERLLNRTKHLKV
          ERSLYET.RARA.FELAIDQPALD.PELLWKAYIDFEISEGEFERTRALYERLLNRTKHL..
Retrocopy ERSLYETERARAVFELAIDQPALDIPELLWKAYIDFEISEGEFERTRALYERLLNRTKHLNM

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_36 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,