RetrogeneDB ID: retro_stub_75

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:11590389..11591118(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400037204
• Aliases: None
• Description: None

Sequence

>retro_stub_75
ATGAATAAAAGAATGCAAGATATTTTGGTTGTTGAGGTAGCGAATGACAAAGGTATTCAAGGGATCTCCAAGGAAAGGGT
TACCATAACCAGGGAGACAACTAGGCAAAAAAGACTACAACGCTATAAAAAATATGAAAATATTCCTCAATCTGGTGAGA
TATGAGAAAAGGATTGCAAAACCATAAACAAAGAAGATTTACACTATGATTTTAGATTGAATGCAAGATCTATTACATCA
ACGCTCTCTTACCCTAGCTGAGAAATTTGGTTTGGGCGCCTTCTAAGCATGATGTATACCTGATGTCTCATTTTTCTATC
ACTGATTGGTCATCATTGACATGTGCAAAAATTGAAATTCTCAATTTATCACGGGATGTAGCGCCACTAGAGAATCATCC
TGAAAGTTTTTTAGAGGTATTTAAGGAGACATGAGTAAGAACTCTTGCTATGAAAGATAAATTGTTTGTTACTAGTGGAT
TGCATTGACAACTTATCATCAAGTATTTAGATAAGACTTGAGTTTTCTTTTATTCATGCCAACATATGTCGATGATGACA
TTACCACTTCTATTGAGATTAATAACACTGCCAGTGGTGCACTTCATTTAATAGCTTCAAATTATGATTCTAGAGTTAGA
GACTTTGATTTCAAGAAATTTCAACTGTCTAACCATTTCATTTTCCCTAGCTGGTGAATCATACGTCACTCAGCCTTGAT
GGCAATCTC

Alignment

ORF - retro_stub_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.73 %
• Parental protein coverage: 51.15 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MNYRMKDISAVDVRNGRDIQGIPWERAIVTREIRRQRRLQEYQNYENIPQSDETSEKECKTTKKDGLYYD
          MN.RM.DI..V.V.N...IQGI..ER...TRE..RQ.RLQ.Y..YENIPQS.E..EK.CKT..K..L.YD
Retrocopy MNKRMQDILVVEVANDKGIQGISKERVTITRETTRQKRLQRYKKYENIPQSGEI*EKDCKTINKEDLHYD

Parental  FRYNASSVIPTFSHTQ-LRNMISATSKHDVYLLSHFSLMHWSSLTCVKTDILDLSGHVAPCEKHPESHSE
          FR.NA.S...T.S....LRN...A.SKHDVYL.SHFS...WSSLTC.K..IL.LS..VAP.E.HPES..E
Retrocopy FRLNARSITSTLSYPS<LRNLVWAPSKHDVYLMSHFSITDWSSLTCAKIEILNLSRDVAPLENHPESFLE

Parental  GFTHTEVSTLAVNDKLLVAGGLQGELIVKYLDKPGVCFCS-QPTYDDDAITTAIEIKNTASGALHFFASN
          .F..T.V.TLA..DKL.V..GL...LI.KYLDK..V.F.S..PTY.DD.ITT.IEI.NTASGALH..ASN
Retrocopy VFKET*VRTLAMKDKLFVTSGLH*QLIIKYLDKT*VFFYS<MPTYVDDDITTSIEINNTASGALHLIASN

Parental  NDCGVRDFDMETFQLFNH-FHLPWPVNHTSVSPDGRL
          .D..VRDFD...FQL.NH.FH.P..VNHTS.S.DG.L
Retrocopy YDSRVRDFDFKKFQLSNH<FHFP*LVNHTSLSLDGNL

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_75 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	PGSC0003DMG400022250	1 retrocopy	retro_stub_76,
Solanum tuberosum	PGSC0003DMG400037204	1 retrocopy	retro_stub_75 ,