RetrogeneDB ID: retro_stub_30

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:41541054..41541372(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400023114
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400025305
• Aliases: None
• Description: None

Sequence

>retro_stub_30
ATGACTTTCAAGCGAAAGAATGGAGGTCGTAACAAACATAGACGCGACCATGTCAAGTTCATCCGCTACTCTAACTGTGG
AAAATGCTGCCCTAAGGATAAAGCCATCAAGAGGTTCCTTGTGAGGAACATTGTTGAACAAGTTGTTGTACGTAATGTTC
AGAAATCTTGTGCTTTTGATTTGTACACTCTTCTTAAGCTCTATTTGAAGATGCAGTATTGTGTTTCATGTGCAATTCAC
TCCAGGGTGGTTAGAGTCTGTTCTCGTACTGATAGGAGAGTTCGTGAGCCTCCACAACATTTCAAGCCCAAGGAATGA

Alignment

ORF - retro_stub_30 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.29 %
• Parental protein coverage: 79.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACAFELYTLPKLYLK
          MTFKR.NGGRNKH.R.HVKFIR.SNCGKCCPKDKAIKRFLVRNIVEQ..VR.VQ..CAF.LYTL.KLYLK
Retrocopy MTFKRKNGGRNKHRRDHVKFIRYSNCGKCCPKDKAIKRFLVRNIVEQVVVRNVQKSCAFDLYTLLKLYLK

Parental  MQYCVSCAIHSKVVRVRSRTDRRVREPPQRFR
          MQYCVSCAIHS.VVRV.SRTDRRVREPPQ.F.
Retrocopy MQYCVSCAIHSRVVRVCSRTDRRVREPPQHFK

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_30 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g090770	1 retrocopy	retro_bole_5,
Solanum tuberosum	PGSC0003DMG400020566	2 retrocopies	retro_stub_41, retro_stub_88,
Solanum tuberosum	PGSC0003DMG400025305	1 retrocopy	retro_stub_30 ,