RetrogeneDB ID: retro_stub_135

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:23278193..23278701(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400008853
• Aliases: None
• Description: None

Sequence

>retro_stub_135
TTATCCGCAATAGCGGTGTGGATAAGGACCATAGAGCTTGATATTTAACAAATTAAACTACTAATTTAAGATACCATTGG
TCAGGAATGCTTCCGAATAATTAGAAACTGCTTATTACCGTGGAGTCATGGGTATATTATTGGTATACAATGTAACTTAT
GAGTCATCTATTAACAACATCATGAACTGGATTACAAACATTAAAAATATGCTTCCGACAGTTTCAACAAAATTCTTGTC
GGCAGCAAGGCCGACATGGACGAAAGCGAAAATGGTTGTTTCTACTTCCAAAGGTTAAGCACTTGCTAATGAATATGACA
TAATATTCTTAAAAACTAGTGCCAAGAAAAATATGAATGTTGACGGGGTTTTCTTTTTCATAGCTCGGGATATAAAACAA
TGGCTTGCCAAATCTGACTCAAAGGATGAGCCTCAGATGATCAAGATAAATAAACCAGACCAAGGAGCAGGATTTTCACA
GGGTGCCTAAAAATCAGCTTGTTGTGGC

Alignment

ORF - retro_stub_135 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.93 %
• Parental protein coverage: 78.6 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LISIDFKIRTIELDSKRIKLQIWDTAGQERFRTIT-TAYYRGAMGILLVYDVTDESSFNNIRNWIRNIE-
          L..I...IRTIELD...IKL.I.DT.GQE.FR.I..TAYYRG.MGILLVY.VT.ESS.NNI.NWI.NI..
Retrocopy LSAIAVWIRTIELDI*QIKLLI*DTIGQECFRIIR>TAYYRGVMGILLVYNVTYESSINNIMNWITNIK<

Parental  QHASDNVNKILVGNKADMDES-KRAVPTSKGQALADEYGIKFFETSAKTNMNVEEVFFSIARDIKQRLAE
          ..ASD..NKILVG.KADMDES.K..V.TSKG.ALA.EY.I.F..TSAK.NMNV..VFF.IARDIKQ.LA.
Retrocopy KYASDSFNKILVGSKADMDES>KMVVSTSKG*ALANEYDIIFLKTSAKKNMNVDGVFFFIARDIKQWLAK

Parental  SDSKAEPQTIRINQPDQGAGSSQGAQKSACCG
          SDSK.EPQ.I.IN.PDQGAG.SQGA.KSACCG
Retrocopy SDSKDEPQMIKINKPDQGAGFSQGA*KSACCG

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_135 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
Ostreococcus lucimarinus	OSTLU_38767	1 retrocopy	retro_oluc_6,
Solanum tuberosum	PGSC0003DMG400008853	1 retrocopy	retro_stub_135 ,