RetrogeneDB ID: retro_stub_121

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 5:21605132..21605541(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG402025960
• Aliases: None
• Description: None

Sequence

>retro_stub_121
GGAAGAGGATTGAACACCTAAGATAATAAGGAAAAATCAGGCATTTGTGGTGGTGGTGGTGCTGGCCTCTGGCAATGATA
AAATTGATGTCCTTGATAGAGTATTCACACACAATTAGCCGCACATATCCTCTGATCTAAATTTGAATATGAAGAATTAT
GGGTATTGGAAGGTCCAAGATCTGTTAAGGCTTAACTTAAAAATATTTGTGAATGTTCCATTAAGGTCACACACAATTGA
TGATGTCAGAGAGGTTGTACATAAGAATAAAAAGCAAATATTATACTTTTTAAAAAAAGAAAATGGAGGGCTTTTGATAA
TTCTCAACCAAGACTATACAATAAAGATAGTTGAAACTAAAAGCTTATTGAAACTTTTTTTTAGCAAATGAAGTTTCAGT
TTGTGTATA

Alignment

ORF - retro_stub_121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.39 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRGLDTRDNTERSGGRGGGAG-SSGKDKIDALGRLLTRILRHMASELNLNMRNDGYVKVQDLLKLNLKTF
          GRGL.T.DN.E.SG..GGG....SG.DKID.L.R..T....H..S.LNLNM.N.GY.KVQDLL.LNLK.F
Retrocopy GRGLNT*DNKEKSGICGGGGA>ASGNDKIDVLDRVFTHN*PHISSDLNLNMKNYGYWKVQDLLRLNLKIF

Parental  ANVPLRSHTVDDVKEAVRKDNKQ-RFGLLEENGELLIRANQGHTVKIVETESLLKPILSADEVSVCV
          .NVPLRSHT.DDV.E.V.K..KQ.......ENG.LLI..NQ..T.KIVET.SLLK...S....S.C.
Retrocopy VNVPLRSHTIDDVREVVHKNKKQILYFXXXENGGLLIILNQDYTIKIVETKSLLKXXXSK*SFSLCI

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_121 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
Arabidopsis thaliana	AT2G45330	1 retrocopy	retro_atha_6,
Solanum tuberosum	PGSC0003DMG402025960	1 retrocopy	retro_stub_121 ,