RetrogeneDB ID: retro_stub_34

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 8:41075517..41076456(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400025534
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400018466
• Aliases: None
• Description: None

Sequence

>retro_stub_34
ATGGAAAAGTACATAATAATTAAGGAAGTTGGTAATGGTACATTTGGGAATGTGTGGCGAGCTTTGAATAAACAGACGGG
TGAAGTGGTTGCAATTAAGAAAATGAAGAAGAATTATTATTCATGGGAAGAATGCATCAACTTGAGAGAAGTCAAGTCAT
TGAGGAGAATGAGCCATCCAAATATAGTTAAGCTCAAAGAAGTTATTAGAGAGAATGACATATTATACTTTGTGTTTGAA
TACATGGAGTGCAACTTATATAACCTTATGGAGAATAGGCCTCATCTTTTCTTAGAATCACAAGTCAGAAATTGGTGCTT
CCAAATATTTCAAGGTCTTGCATCCATCCATCAACGAGGATACTTTCATCGCGATCTTAAGCCAGAGAACTTGTTGGTTT
CAAAAGATCATACTATAAAAATTGCTGATTTTGGTCTAGCTAGGGAGATCAATTCTCAGCCCCCATATACTGAATATGTC
TCAACACGCTGGTATCGTGCCCCTGAAGTTCTTTTACAATCACCAATATATGGTCCTGCTGTTGATATGTGGGCAATGGG
TGCAATAATAGCTGAGTTATTAACTCTTCGTCCTCTATTCCCTGGTTTGAGTGAAGCAGATGAGATTTACAGAATATGCA
GTGTTATAGGTACTCCATCAAAGAGTGAATGGGCTCATGGACACGAACTTGCTGGTGCTATCAACTACCAGTTTCCGCAG
ATCTGTGGTGTAACTCTGTCTAAAGTACTCCCATATGTTAGTGAGGATGCAATTAATCTAATAACTTGGCTTTGTTCGTG
GGATCCTTGCAAGAGGCCAACAGCGGTGGAAGTTCTTCAGCACCGTTTCTTTCAGAGTTGCTTTTATGTACCTCCATCAT
TATGCTCTAACACTGCTGTTGCTCCCTCTGTTGGAATTAGGGCAAAACCCTTAGTATAA

Alignment

ORF - retro_stub_34 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.71 %
• Parental protein coverage: 69.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MERYKVIKEVGNGTFGSVWRALNKQSGEVVAIKKMKKKYYSWEECINLREVKSLRKMSHPNIVKLKEVIR
          ME.Y..IKEVGNGTFG.VWRALNKQ.GEVVAIKKMKK.YYSWEECINLREVKSLR.MSHPNIVKLKEVIR
Retrocopy MEKYIIIKEVGNGTFGNVWRALNKQTGEVVAIKKMKKNYYSWEECINLREVKSLRRMSHPNIVKLKEVIR

Parental  ENDILYFVFEYMECNLYHLMKDRPKLFLESEVRNWCFQIFQGLANMHQRGYFHRDLKPENLLVSKD-TIK
          ENDILYFVFEYMECNLY.LM..RP.LFLES.VRNWCFQIFQGLA..HQRGYFHRDLKPENLLVSKD.TIK
Retrocopy ENDILYFVFEYMECNLYNLMENRPHLFLESQVRNWCFQIFQGLASIHQRGYFHRDLKPENLLVSKDHTIK

Parental  IADFGLAREINSKPPYTEYVSTRWYRAPEVLLQSPIYGPAVDMWAMGAIMAELLTLRPLFPGSSEADEIY
          IADFGLAREINS.PPYTEYVSTRWYRAPEVLLQSPIYGPAVDMWAMGAI.AELLTLRPLFPG.SEADEIY
Retrocopy IADFGLAREINSQPPYTEYVSTRWYRAPEVLLQSPIYGPAVDMWAMGAIIAELLTLRPLFPGLSEADEIY

Parental  KICSVIGTPSKSEWAHGNELAGAINYQFPQIPGVNLSVLLPSASEDAINLITSLCSWDPCKRPTAVEVLQ
          .ICSVIGTPSKSEWAHG.ELAGAINYQFPQI.GV.LS..LP..SEDAINLIT.LCSWDPCKRPTAVEVLQ
Retrocopy RICSVIGTPSKSEWAHGHELAGAINYQFPQICGVTLSKVLPYVSEDAINLITWLCSWDPCKRPTAVEVLQ

Parental  HRFFQSCFYVPPSLRSKTAVARTPPSAGMK
          HRFFQSCFYVPPSL.S.TAVA...PS.G..
Retrocopy HRFFQSCFYVPPSLCSNTAVA---PSVGIR

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_34 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400018466	1 retrocopy	retro_stub_34 ,
Solanum lycopersicum	Solyc08g005470.2	1 retrocopy	retro_slyc_24,
Vitis vinifera	VIT_02s0033g01110	1 retrocopy	retro_vvin_73,