RetrogeneDB ID: retro_stub_140

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:33985905..33986190(-)
• 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_140
ATGGGTATTCCAAAGATTTCAAATGACACTGACTTGCTTCACCCTCCTGCTGAGATTGAGAAGCAAAAGCACAAGCTTAT
GCGTTTAGTCCAATCACCTAATTCTACTTTTCTGGATGTTAAATGTCAAGGTTGCTTCCATATAACAACAATTTTCAGCC
ACTCGCAAACCGTGGTTACATTCCTCAATTGCTAGCAAGTGCTATTCCAGCCAACTGGTGGCCGCGCAAAACTTATTGAA
GGATGCTCTTTTAGGGTTAAAGAGAAGGATATGATGGTCTTGGGT

Alignment

ORF - retro_stub_140 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.47 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGIPKISNDTDLLHPPAELEKQNHKLKRLVQSPNSTFLDVKCQGCFQITTIFSHSQTVVTCPNCQQVLCQ
          MGIPKISNDTDLLHPPAE.EKQ.HKL.RLVQSPNSTFLDVKCQGCF.ITTIFSHSQTVVT..NC.QVL.Q
Retrocopy MGIPKISNDTDLLHPPAEIEKQKHKLMRLVQSPNSTFLDVKCQGCFHITTIFSHSQTVVTFLNC*QVLFQ

Parental  PSGGRAKLTEGCSFRVKEKDMMVLG
          P.GGRAKL.EGCSFRVKEKDMMVLG
Retrocopy PTGGRAKLIEGCSFRVKEKDMMVLG

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_140 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 ,