RetrogeneDB ID: retro_stub_103

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 2:46235070..46235418(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400013510
• Aliases: None
• Description: None

Sequence

>retro_stub_103
GGCTATGCTATTGGTACTTTAAAGGAGCACCGTCCTCTTGTCGATCAAATTCGAAAGAGATACGGTCAACAAATTCGTAA
ATCCTATGGTTTTGATTTTTATGATTATCCCGGTGGGGAAGTTCTAATAGAACCAATTTTAAATGTCAAGGAGGACGCTG
ACTTTGGGATAATGATGAAATTTGCTAACCGTGCCATTCAAAAACACAATGAGAAAGAGCACAATGTTTTTTAAAAGTAC
AAGGTTTTGAAGATTGAGAAAGCGAATGTTATGATAGGGGGATACGAACAGTCATATTTCATGATTGTTAAAGTTTTAAA
TCTCACTCTTGGTACTTGTATTGAAACC

Alignment

ORF - retro_stub_103 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.76 %
• Parental protein coverage: 52.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GYAIGTLKEHRPYIDQIRIKYFQQIHESYGFDFYDFPGGEVQIEPILNVKDDADFGIMMKLANRAIQEYN
          GYAIGTLKEHRP..DQIR..Y.QQI..SYGFDFYD.PGGEV.IEPILNVK.DADFGIMMK.ANRAIQ..N
Retrocopy GYAIGTLKEHRPLVDQIRKRYGQQIRKSYGFDFYDYPGGEVLIEPILNVKEDADFGIMMKFANRAIQKHN

Parental  EKELNVF-KYKVLKIEKANCMIGGYEQ-YFMTVKVLNLTIGTSIET
          EKE.NVF.KYKVLKIEKAN.MIGGYEQ.YFM.VKVLNLT.GT.IET
Retrocopy EKEHNVF*KYKVLKIEKANVMIGGYEQSYFMIVKVLNLTLGTCIET

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_103 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	PGSC0003DMG400013510	1 retrocopy	retro_stub_103 ,
Solanum tuberosum	PGSC0003DMG400028064	1 retrocopy	retro_stub_27,