RetrogeneDB ID: retro_stub_151

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 9:646921..647079(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400011024
• Aliases: None
• Description: None

Sequence

>retro_stub_151
GTGAGCTTTGAAGTACTTTTAAATGGCATCAAGAATTGATCTTCAGGTTTCCAAAGATTTGCCGTAAGGACCTCGAGGAG
AATAAAAGATTTATCTAAAATGGTTGAGCAAACGAAGAAGGAATTGCTAACCATATGAAGGATGCGTCCAAATAATTT

Alignment

ORF - retro_stub_151 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 55.56 %
• Parental protein coverage: 72.22 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VANELIVNGLSN-SASFQRFAVRTSKRMEDLSKMAQQKRQE-IADQVKDVSKNF
          V..E...NG..N.S..FQRFAVRTS.R..DLSKM..Q...E.IA...KD.SK.F
Retrocopy VSFEVLLNGIKN*SSGFQRFAVRTSRRIKDLSKMVEQTKKE<IANHMKDASK*F

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_151 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400011024	1 retrocopy	retro_stub_151 ,
Vitis vinifera	VIT_08s0105g00510	3 retrocopies	retro_vvin_12, retro_vvin_17, retro_vvin_25,