RetrogeneDB ID: retro_stub_27

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 11:11123805..11124453(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400000883
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400028064
• Aliases: None
• Description: None

Sequence

>retro_stub_27
ATGGGGGAGAATAGGCAACAACCACGAGGAGGAAGCACAGAAGGATCGAGGAAGAAGACGACTGAAGAAGAGTTTTTCAA
GTTTATCAAACAAGGAAATGGATACCTCTGCGGGAGGAAACGAGGCCCAGTAAACATCCGTGACTCCGACGTAGATCTTC
CCAACGGTGCTTTGCCGGAACATCGCTATCAATTTAAAGAAATTTGGGAATGTTACTTTAATCAACTTAACTCAACCAAT
GGTATGGACCTTGATACTTTTCCTGGTGATGCTGAGGTCGCTAATACATTGCCATCTAACTTGAATGCACTCAAGGAGGA
AGACAAGGAGTATCAGTTAATCACGGATCTAGCTCATCTTGCTATCGATGAATGCAACAAAGAGTCTATCCTTTATAAGT
ACAAGTTTTTGAAGATTGAGAAATTAAACTTACGCCTGACGGGATATATGGAATATTTCATGACTGTAAAAGTCAAGAAT
CTCACTCTTGCTACTGTTTACGAAACTTTTCAAATACACGCAGGTGCACATCCAGCTGATTTTGCTAAAAGAATATTTTC
TTGTCTCCCAAAAGGAGGGGCATTGCCATTGCCATTGCCAAGCCTAGAGGAGGTTTCAGTCGATACCGTTCCGTCCAAAT
CCACATAA

Alignment

ORF - retro_stub_27 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.31 %
• Parental protein coverage: 54.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DDDPDRISDGALVEHRPHFADIWRRYDAQLQTTNGMDLDTFPGCSMLVDAYPINMSD-PTTGEEAMIIYE
          D.D.D....GAL.EHR..F..IW..Y..QL..TNGMDLDTFPG........P.N.........E...I..
Retrocopy DSDVD-LPNGALPEHRYQFKEIWECYFNQLNSTNGMDLDTFPGDAEVANTLPSNLNALKEEDKEYQLITD

Parental  LVDLALDIYNHDESNLFKYKFINVEKVNTRLTGYAEFFITVKFLNVTLATVVETFQIYAG
          L..LA.D..N..ES.L.KYKF...EK.N.RLTGY.E.F.TVK..N.TLATV.ETFQI.AG
Retrocopy LAHLAIDECNK-ESILYKYKFLKIEKLNLRLTGYMEYFMTVKVKNLTLATVYETFQIHAG

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_27 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 ,