RetrogeneDB ID: retro_stub_84

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:46864436..46865009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400021238
• Aliases: None
• Description: None

Sequence

>retro_stub_84
AATAAATATCCTGCAGAGGTCTTCAACAATGAAAATCATAGGCTAAACCTTTATGGAGATAACGTTGAGGTAGATTATCG
AGGTTATGAAGTAACAGTTGAAAATTTTCTGATGGTGCTGACTGGACGTCACGAAACAGCTGTCCCAAGATCAAAACGTC
TTCTTAGTGATGAAGGAAGCCACATACTTCTGTACATGACAGGGTATGGCGGAGACGAGTTTTTAAAGTTTCAGGATTCA
TAAGAACTTCAAAGTCATGATTTAATTGATGCAGTGAAACAAATGAAAGAAAAGTGTAGCTTCAAGGAGCTGCTAATAAT
GGTTGACACTTGTCAAGCTGCTACTCTTTTCTCTCAGCTTCAATCACCTGGTGTATTGACAATTGGGAGTAGCATGAAAG
GAGAAAATTCATACTCGCATCACTTGGATGCTGATGTTGGCGTCTCAGTTATTGATCGATTCACATTTTATACTCTTGCA
TTTTTTAAGAGGGTGAACATGTATGATAATGCCTCATTGGGCAATCTTTTCAGTTCATATAATCCAAATACACTGATGTC
ATCTGCATATTAT

Alignment

ORF - retro_stub_84 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.76 %
• Parental protein coverage: 59.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKYPAQVFNNENHRLNLYGDNVEVDYRGYEVTVENFLRVLTGRHETAVPRSKRLLSDEGSHILLYMTGHG
          NKYPA.VFNNENHRLNLYGDNVEVDYRGYEVTVENFL.VLTGRHETAVPRSKRLLSDEGSHILLYMTG.G
Retrocopy NKYPAEVFNNENHRLNLYGDNVEVDYRGYEVTVENFLMVLTGRHETAVPRSKRLLSDEGSHILLYMTGYG

Parental  GDEFLKFQDSEELQSHDLADAVKQMKEKRRFKELLIMVDTCQAATLFSQLQSPGVLTIGSSMKGENSYSH
          GDEFLKFQDS.ELQSHDL.DAVKQMKEK..FKELLIMVDTCQAATLFSQLQSPGVLTIGSSMKGENSYSH
Retrocopy GDEFLKFQDS*ELQSHDLIDAVKQMKEKCSFKELLIMVDTCQAATLFSQLQSPGVLTIGSSMKGENSYSH

Parental  HLDADVGVSVIDRFTFYTLAFFERVNMYDNASLGSLFSSYNPNTLMSTAYY
          HLDADVGVSVIDRFTFYTLAFF.RVNMYDNASLG.LFSSYNPNTLMS.AYY
Retrocopy HLDADVGVSVIDRFTFYTLAFFKRVNMYDNASLGNLFSSYNPNTLMSSAYY

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_84 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400021238	2 retrocopies	retro_stub_53, retro_stub_84 ,