RetrogeneDB ID: retro_stub_31

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:50799712..50800834(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG402017288
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400029857
• Aliases: None
• Description: None

Sequence

>retro_stub_31
ATGAATGCTTCAAATCTATTGTTGATCAGTGCAACAACAGCACTAGCAATTATCTCATTAGTTTTTGCATTTGACAACGA
AAATGTTTTGAAACCACCTCATATACCAGGCTCCCAAAATCTCCTCACAAAATCCGAAATCATTCAATTTAAAGGAGCAG
TTGGACCAGAGAGTATTGCTTTCGATCCAAATGGAGAAGGTCCCTATACAGGAGTTGCCGATGGACGAATTCTCAAGTGG
AAAGGATCATATTGGTCTGATTTTGCAGTTACCTCTTCTCATAGGAAGAATTGTACCCTGCCTTTTGCTCCTGAATTGGA
GCATATATGTGGAAGGCCATTAGGCTTACGATTCGATACCAAAACAGGGGATTTATACATTGCTGATGCATATTTCGGGG
TCCAAGTTGTTGGACCAAAAGGAGGACTAGCTACACCATTAGTCCAAAAATTCGAAGGTAAGCCTCTGGTCTTCACAAAT
GACATTGACATTGATGATCATGACGATGTGATTTACTTCACGGAAACAAGCACAAAGTATCAACGCAGGCAATTTTTCGC
CTCTCTTTTAAGCGGAGATAAGACAGGCATGCTAATGAAATATGTTAAATCCACACAACAAACCAAAATTTTAATAAGAG
GCCTTGCTTTTGCGAATGGTGTAGCATTGAGCAAAGACAAGTCCTTCGTGCTCGTAGCTGAAACTTCTACCGGTAGAATT
TTCAGATATTGGCTAAAAGGTCCTTACAAGGGAAAACATGATACATTTGCTGAGTTACCGGGATTTCCAGACAACATCAG
GATGAATCCGAGAGGGGATTTTTGGGTTGCTCTGCATGCAAAGAGATCATTATTTGCACAATTGAGTATTTCGGATTTAG
AGCTCGGGAAGGCATTGTTGAAGCTCCCGATCACCGCGCAACAACTTGACAACTTGTTAGCCGGAGGGCAGCCACACGCT
ACCGCAATCAAGCTAAGCGAAGACGGGCAAGTTTTGGAGGTTTTAGAAGATGTTGAAGGCAAGACATTGAGGTCGATTAG
TGAAGTTCAAGAGAAACAGGGCAAGTTGTGGTTTGGTTCTGTTTTGATGCCTTTTTTGGGCGTTTATGGATTACAAGTTT
AA

Alignment

ORF - retro_stub_31 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.24 %
• Parental protein coverage: 99.73 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNATKLILSAA--AVAIITALLTLSSKNVYSPPSIPGSKDLLSKSEVIHLKGAVGPESVAFDPNGEGPYT
          MNA..L.L..A..A.AII.........NV..PP.IPGS..LL.KSE.I..KGAVGPES.AFDPNGEGPYT
Retrocopy MNASNLLLISATTALAIISLVFAFDNENVLKPPHIPGSQNLLTKSEIIQFKGAVGPESIAFDPNGEGPYT

Parental  GVADGRILKWNGDSDGWVDFAVTSSQRKQCVHPFAPQMEHVCGRPLGLRFDTRTGDLYVADAYLGLHVVG
          GVADGRILKW.G....W.DFAVTSS.RK.C..PFAP..EH.CGRPLGLRFDT.TGDLY.ADAY.G..VVG
Retrocopy GVADGRILKWKGSY--WSDFAVTSSHRKNCTLPFAPELEHICGRPLGLRFDTKTGDLYIADAYFGVQVVG

Parental  PSGGLATSLVTEVEGQHLRFTNDLDIDEQEDVIYFTDTSTQFQRRQFIASVVSGDKTGRLMKYDISTKAV
          P.GGLAT.LV...EG..L.FTND.DID...DVIYFT.TST..QRRQF.AS..SGDKTG.LMKY..ST...
Retrocopy PKGGLATPLVQKFEGKPLVFTNDIDIDDHDDVIYFTETSTKYQRRQFFASLLSGDKTGMLMKYVKSTQQT

Parental  TVLLRGLAFANGVALSKDKSFVLVAETTTCRVVRHWLKGPHAGKHDTFADLPGYPDNIRRNSRGEFWVGL
          ..L.RGLAFANGVALSKDKSFVLVAET.T.R..R.WLKGP..GKHDTFA.LPG.PDNIR.N.RG.FWV.L
Retrocopy KILIRGLAFANGVALSKDKSFVLVAETSTGRIFRYWLKGPYKGKHDTFAELPGFPDNIRMNPRGDFWVAL

Parental  HSKRSLLAKLVTSNSWLGKTILKLPFTFQQLHFLLVGGQPHATAIKLSEDGQVLEVLEDLESKTLKFISE
          H.KRSL.A.L..S...LGK..LKLP.T.QQL..LL.GGQPHATAIKLSEDGQVLEVLED.E.KTL..ISE
Retrocopy HAKRSLFAQLSISDLELGKALLKLPITAQQLDNLLAGGQPHATAIKLSEDGQVLEVLEDVEGKTLRSISE

Parental  VEEKNGKLWIGSVLVPFIGVHEL
          V.EK.GKLW.GSVL.PF.GV..L
Retrocopy VQEKQGKLWFGSVLMPFLGVYGL

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_31 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400029857	1 retrocopy	retro_stub_31 ,
Solanum lycopersicum	Solyc10g079610.1	1 retrocopy	retro_slyc_20,