RetrogeneDB ID: retro_stub_76

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:11594224..11594910(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400022250
• Aliases: None
• Description: None

Sequence

>retro_stub_76
AGAATGTAAGATATTTCGGTTGCTAAGGTAAGGAAGGGCAAAGATATTGAATGGATCATGTGGGAAAGGGTTACCATAGC
CAGGAAGACAACTAGGAAAAGAAGACTGCAACGCTATCGGAACTATCAAAATTTTCCTTAATCTTGTGATACATCATAAA
AGGAGTTCAAAACCATAAAGAAAGACAGATTATACTATGATTTCAGATGGAATGCAAGATCCATTACATCAACGTTCTCT
CACCCCTACTAAGGAATGCAGTCTGGGCACCTTCTAAACATTATGTGTACTTGATGCCTCATTTTTCTCTAATTGGTCAC
CATTGTCCTGCATAAAAAATTAAAATTCTTAATTTATCTGGGCATGTAGCACCACTCAAGAAACATCTCGAAAGCCTTTC
AGATGGATTTACGAAGACTCGAGTAAGTATTTCTGGTGTGAAAGATAAGTTGCTTGTTGGTGGTGGATTGTAAAGAGAAC
TTATCATCAAGTAGTTAGGTAAGCCTGGAGTTTGCTTTTCTTCTCCCCGACGTATGATGATGATAAAATTACCCACTGTT
ATTGAGATTAACAACACTGCTAGTGGTGCACTTCATTTGATAATTTAAAATAATAATTCTTGAGTTATAGATTTTGATTT
GGAGAAATTTCAACTGTCGAACCGTTTCCAGTTTCCCTAGCCAGTG

Alignment

ORF - retro_stub_76 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.23 %
• Parental protein coverage: 52.97 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  RMENVSASDVRSGAKDIQGIPWNTKT-TRKEVRQRKLRIYGNRGRNIPQSGETSDKEHKTIKKDCLY-DF
          RM...S...VR.G.KDI..I.W...T..RK..R.R.L..Y.N...N.P.S..TS.KE.KTIKKD.LY.DF
Retrocopy RM*DISVAKVRKG-KDIEWIMWERVTIARKTTRKRRLQRYRNY-QNFP*SCDTS*KEFKTIKKDRLYYDF

Parental  RWYAGSVRPSFSNSR-LRNMVWATSKHDVY-LMSNFSAVHWSSLTCTKT-EILDFSGHIVPLEKHPKSFP
          RW.A.S....FS....LRN.VWA.SKH.VY.L...F....WS.L.C.K...IL..SGH..PL.KH..S..
Retrocopy RWNARSITSTFSHPY<LRNAVWAPSKHYVY<LDASFFS-NWSPLSCIKN>KILNLSGHVAPLKKHLESLS

Parental  EGFTATRVSTLAVKDKLLLAGGLQGELIVKYLDKPGVSFC-FRPTYDDDDDAITTC-IEINNSASGALHF
          .GFT.TRVS...VKDKLL..GGL..ELI.K.L.KPGV.F..F.PTY..DDD.IT.C.IEINN.ASGALH.
Retrocopy DGFTKTRVSISGVKDKLLVGGGL*RELIIK*LGKPGVCFS<FSPTY--DDDKITHC>IEINNTASGALHL

Parental  IVSYNDSGVREFDMETFQQSNYFHFNLPV
          I...N.S.V..FD.E.FQ.SN.F.F..PV
Retrocopy II*NNNS*VIDFDLEKFQLSNRFQFP*PV

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_76 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,