RetrogeneDB ID: retro_stub_24

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:63341674..63342154(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400005192
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG401005911
• Aliases: None
• Description: None

Sequence

>retro_stub_24
ATGGCGGAGCAGACGGAGAAGGCGTTTTTGAAGCAGCCAGGTGTGTTTCTAAGCTCTAAGAAGACCGGGAAGGGAAAGAG
GCCAGGAAAGGGAGGCAATCGATACTTCAAAAGTATCGTCTTAGGATCCAAGACTCCTCGTGAGGCTACTGAAGGTACGT
ATATTGACAAGAAATGCCCATTCACTGGCAATGTTTCTATCCGAGGTCGTATCCTTGTTGGTACATGCCACAGTGCTAAG
ATGAACAGAACCATCATCGTTCGACGCAATTACCTACATTATGTCAAGAAGTATAAAAGATATGAGAAGAGGCACTCCAA
TATTCCAGCTCACATATCACCATGCTTCCGTGTGAAAGAGGGAGATCATGTTACTATTGGACAGTGCAGGCCTTTATCCA
AAACCGTGAGGTTCAATGTCTTGAAGGTGATTCCAGCTGGTTCTGGTGGTGGCGGGAAAAAGGCTTTCACCGGGATGTAA

Alignment

ORF - retro_stub_24 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.48 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAEQTEKAFLKQPGVFLSSKKTGKGKRPGKGGNRYFKSIGLGFKTPREATEGTYIDKKCPFTGNVSIRGR
          MAEQTEKAFLKQPGVFLSSKKTGKGKRPGKGGNRYFKSI.LG.KTPREATEGTYIDKKCPFTGNVSIRGR
Retrocopy MAEQTEKAFLKQPGVFLSSKKTGKGKRPGKGGNRYFKSIVLGSKTPREATEGTYIDKKCPFTGNVSIRGR

Parental  ILAGTCHSAKMNRTIIVRRNYLHYVKKYQRYEKRHSNIPAHISPCFRVKEGDHVTIGQCRPLSKTVRFNV
          IL.GTCHSAKMNRTIIVRRNYLHYVKKY.RYEKRHSNIPAHISPCFRVKEGDHVTIGQCRPLSKTVRFNV
Retrocopy ILVGTCHSAKMNRTIIVRRNYLHYVKKYKRYEKRHSNIPAHISPCFRVKEGDHVTIGQCRPLSKTVRFNV

Parental  LKVIPAGSGGGGKKAFTGM
          LKVIPAGSGGGGKKAFTGM
Retrocopy LKVIPAGSGGGGKKAFTGM

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_24 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG401005911	1 retrocopy	retro_stub_24 ,