RetrogeneDB ID: retro_stub_80

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:88578350..88578640(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400007336
• Aliases: None
• Description: None

Sequence

>retro_stub_80
ACCAACCAGCCAAGGAAGAGAACGTTAAGAAGTTCAGCTACAATGGAGTAGATCTGGATTCTCTTCTTGACATGTACACT
GATGAGCTTGTTAAGTTTTTTCGTGCTCGTCCTCGCAGAAGGTTTTAGAGGGGTTTGAAGAGGAAGCCTATGGCTTTGAT
CAAGAAGCTCCACATGGTGGAACGTGAGACCCTACCAGGTGAGAAGCCAAAGGTTGTGAGAACACATTTGAGGAACATGA
TCATTGTTTCTGAGATGATTGTAAGCGTTATTGGTATCTACAATGGAAAA

Alignment

ORF - retro_stub_80 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 64.24 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TGQPRKRTF-KKFSYRGVDLDSLLDMSTDELVKLFPARPRRRFQRGLKRKPMALIKKLRKAKREAPPGEK
          T.QPRKRT..KKFSY.GVDLDSLLDM.TDELVK.F.ARPRRRF.RGLKRKPMALIKKL....RE..PGEK
Retrocopy TNQPRKRTL<KKFSYNGVDLDSLLDMYTDELVKFFRARPRRRF*RGLKRKPMALIKKLHMVERETLPGEK

Parental  PEVVRTHLRNMIIVPEMIGSVIGIYNGK
          P.VVRTHLRNMIIV.EMI.SVIGIYNGK
Retrocopy PKVVRTHLRNMIIVSEMIVSVIGIYNGK

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_80 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G04270	1 retrocopy	retro_atha_20,
Brassica oleracea	Bo5g004420	1 retrocopy	retro_bole_33,
Brassica rapa	Bra032519	1 retrocopy	retro_brap_20,
Arabidopsis lyrata	fgenesh2_kg.1__358__AT1G04270.1	1 retrocopy	retro_alyr_8,
Medicago truncatula	MTR_1g070450	1 retrocopy	retro_mtru_46,
Solanum tuberosum	PGSC0003DMG400007336	1 retrocopy	retro_stub_80 ,
Solanum lycopersicum	Solyc02g082000.2	1 retrocopy	retro_slyc_75,
Triticum aestivum	Traes_2AL_52D3F9AF41	1 retrocopy	retro_taes_67,