RetrogeneDB ID: retro_stub_53

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:19682662..19683397(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400011666
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_stub_53
ATGGATTCCACTATGAATTCCACATATCTATTGTGCTTTCTTCTTTTCTCTACTTATCTGAGCTATGGGGTCGCGTCAAG
TTCATATGCGACCAATACGATGCATACTAACAAGTGGGCTGTTTTGGTCTGCACTTCTTATTTCTGGTTTAACTACAGAC
ACATGGCTAACACTTTGTCTTTATACAGAACTGTAAAACGATTAGGCATACCTGATGAAAAAATTATTCTGATGTTGGCT
GATGATATGGCTTGCAATACTCGAAATAAATACCCTGCACAGGTCTTCAACAATGAAAATCATAGGCTAAACCTTTATGG
AGATAACGTTGAGTTAGATTATCGAGGTTATGAAGTAACAGTTGAAATTTTTCTGATGGTGCTGACTGGACGTCACGAAA
CAGCTGTCCCAAGGTCAAAACATCTTCTTAGTGATGAAGGAAGCCACATACTTCTGTACATGACAGGGTATGGCGGAGAC
GAGTTTTTAAAATTTCAGGATTCAGAAGAACTTCAAAGTCATGATTTAACTGATGCAGTGAAACAAATGAAAGAAAAGTG
TAGATTCAAGGAGCTGCTAATAATGGTTGACACTTGTCAAGCTGCTACTCTTTTCTCGCAGCTTCAATCACCTGGCGTAT
TGACAATTGGGAGTAGCATGAAAGGAGAAAATTCATACTCGCATCACTTGGATGCTGATGTTGGCGTCTCAATTATTGAT
TTTTTGAGAGGGTGA

Alignment

ORF - retro_stub_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.75 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDSTMNSTFVLCFLLFSTYLSYGVASSSSATTTMHTNNWAVLVCTSRFWFNYRHMANTLSLYRTVKRLGI
          MDSTMNST..LCFLLFSTYLSYGVASSS.AT.TMHTN.WAVLVCTS.FWFNYRHMANTLSLYRTVKRLGI
Retrocopy MDSTMNSTYLLCFLLFSTYLSYGVASSSYATNTMHTNKWAVLVCTSYFWFNYRHMANTLSLYRTVKRLGI

Parental  PDERIILMLADDMACNTRNKYPAQVFNNENHRLNLYGDNVEVDYRGYEVTVENFLRVLTGRHETAVPRSK
          PDE.IILMLADDMACNTRNKYPAQVFNNENHRLNLYGDNVE.DYRGYEVTVE.FL.VLTGRHETAVPRSK
Retrocopy PDEKIILMLADDMACNTRNKYPAQVFNNENHRLNLYGDNVELDYRGYEVTVEIFLMVLTGRHETAVPRSK

Parental  RLLSDEGSHILLYMTGHGGDEFLKFQDSEELQSHDLADAVKQMKEKRRFKELLIMVDTCQAATLFSQLQS
          .LLSDEGSHILLYMTG.GGDEFLKFQDSEELQSHDL.DAVKQMKEK.RFKELLIMVDTCQAATLFSQLQS
Retrocopy HLLSDEGSHILLYMTGYGGDEFLKFQDSEELQSHDLTDAVKQMKEKCRFKELLIMVDTCQAATLFSQLQS

Parental  PGVLTIGSSMKGENSYSHHLDADVGVSVID
          PGVLTIGSSMKGENSYSHHLDADVGVS.ID
Retrocopy PGVLTIGSSMKGENSYSHHLDADVGVSIID

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_53 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 1 parental gene, and 2 retrocopies.

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