RetrogeneDB ID: retro_stub_138

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:56722339..56722624(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG401028933
• Aliases: None
• Description: None

Sequence

>retro_stub_138
ATGGGTATTCCAAAGATTTCAAATGTCACTGACTTGCTTCACCCTCCTGCTGAGCTAGAAAAGCAAAAGCACAAGCTTAT
GTGTTTGGTCCAATCACCTAATTCTACTTTTCTGGATGTCAAATATCAAGGTTGCTTCCAAATAACAACAATTTTCAGCC
ACTCGCAAACTGTGGTTACATGCCCCAATTGCCAGCAAGTGTTATGCCAGCCAACTGGTGGCCGCGCAAATCTTACTGAA
GGATGCTCTTTTAGGGTTAAAGAGAAGGATATGATGGTCTTGGGT

Alignment

ORF - retro_stub_138 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.63 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGIPKISNDTDLLHPPAELEKQNHKLKRLVQSPNSTFLDVKCQGCFQITTIFSHSQTVVTCPNCQQVLCQ
          MGIPKISN.TDLLHPPAELEKQ.HKL..LVQSPNSTFLDVK.QGCFQITTIFSHSQTVVTCPNCQQVLCQ
Retrocopy MGIPKISNVTDLLHPPAELEKQKHKLMCLVQSPNSTFLDVKYQGCFQITTIFSHSQTVVTCPNCQQVLCQ

Parental  PSGGRAKLTEGCSFRVKEKDMMVLG
          P.GGRA.LTEGCSFRVKEKDMMVLG
Retrocopy PTGGRANLTEGCSFRVKEKDMMVLG

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_138 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00049p00194290	1 retrocopy	retro_atri_30,
Aegilops tauschii	F775_26813	1 retrocopy	retro_atau_70,
Solanum tuberosum	PGSC0003DMG401028933	3 retrocopies	retro_stub_137, retro_stub_138 , retro_stub_140,