RetrogeneDB ID: retro_stub_79

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:88321378..88321668(+)
• Located in intron of: PGSC0003DMG400014661

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400008674
• Aliases: None
• Description: None

Sequence

>retro_stub_79
AAGAGAAAGGAAGAGGGTGAGTATGCTCCTGGAGGCAACCATTCTCCTAAGAGACTATCCTCCAGAACCGATGATTCTGA
AGTTGCCGATCACGTCGTAGTTTGTTAGATTTCTAAGAATCGGAAAGTGCCAGTTAGGAACTTCAGAGGGAAGAGTATGA
TGGACATTTGAGAGTGTTATTTTGAGATGGAGCAAATGCGAGTAATAAAGGCATCTCATTGAGTATGCATTTGTGGAATG
TTCTCAGAGATCATGCAGATGAAATTGATAAGGTTGTTTCTGAGAAAAAT

Alignment

ORF - retro_stub_79 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.59 %
• Parental protein coverage: 94.17 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRKEENEYASEGDNPPKK-ASRTDDSDDEDGIVVCEISKNRRVTVRSFGGRIMVDIREFYVK-DGKQMPG
          KRKEE.EYA..G...PK...SRTDDS...D..VVC.ISKNR.V.VR.F.G..M.DI.E.Y...DG.....
Retrocopy KRKEEGEYAPGGNHSPKRLSSRTDDSEVADHVVVC*ISKNRKVPVRNFRGKSMMDI*ECYFE<DGAN-AS

Parental  RKGISLSMDQWNVLREHADEIDEAVAENS
          .KGISLSM..WNVLR.HADEID..V.E..
Retrocopy NKGISLSMHLWNVLRDHADEIDKVVSEKN

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_79 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	PGSC0003DMG400008674	1 retrocopy	retro_stub_79 ,
Solanum lycopersicum	Solyc02g061790.2	1 retrocopy	retro_slyc_53,