RetrogeneDB ID: retro_stub_40

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 7:54444631..54445267(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400001035
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400029389
• Aliases: None
• Description: None

Sequence

>retro_stub_40
ATGGAGGCTTGTAGCAGAGCTGCAGTGGTGGGTTCTTCTCTTCAGCAATCTGTTTGGGTTAAGGGATCAACTTTCCCTTT
AAAGGGTGAAGTGAAACTTAATAGGGTCAAATTATGGTCTGTTAAGCCTTGCAAAGCCTCTCAACTTGAAGGGAGCTTGG
TTTCAAGAAGGCCTCCTTCTTCAGTTTCTGTTCCTATCCCAGAAATGGAAAGTGCTGGGAACAACTTTATAGATTATGGA
TTGGGTGAAGCTGATCCTGAAGTTCGTGGTATTATTGACAAAGAGAAGGAACGTCAATTTCGAAGCTTAGAGCTTATTGC
CTCTGAGAATTTCACATCTCGAGCAGTGATGGAGGCAGTTGGTTCTTGCCTTACAAACAAATACTCCGAAGGACTACCAG
GCAAAAGATATTATGGTGGAAACGAGTACATTGATGAGTTAGAAATACTTTGTCAAGAGAGGGCTTTGGCAACTTTTAGC
TTAGATGGAAAACAGTGGGGTATCAATGTTCAACCCCTACCTGGTTCTCCAGCAAATTTTGAAGTCTACACAGCAGTTCT
CAATCCACATGACCGGATTATGGGATTGGACTTGCCTCATGGGGGGTCATTTGTCCCATGGATTTATGACTCCTAA

Alignment

ORF - retro_stub_40 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.57 %
• Parental protein coverage: 56.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEACSRAAVMGSSLQQPVWVNGSAFPLKGEVKLNGVKLWSVKPCKASQLEGSLVSGRPPS-VSVPIPEMG
          MEACSRAAV.GSSLQQ.VWV.GS.FPLKGEVKLN.VKLWSVKPCKASQLEGSLVS.RPPS.VSVPIPEM.
Retrocopy MEACSRAAVVGSSLQQSVWVKGSTFPLKGEVKLNRVKLWSVKPCKASQLEGSLVSRRPPSSVSVPIPEME

Parental  GAGNNFADYGLGEADPEVRGIIDKEKERQFRSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYGG
          .AGNNF.DYGLGEADPEVRGIIDKEKERQFRSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYGG
Retrocopy SAGNNFIDYGLGEADPEVRGIIDKEKERQFRSLELIASENFTSRAVMEAVGSCLTNKYSEGLPGKRYYGG

Parental  NEHIDELEILCQERALAAFNLDGKQWGVNVQPLSGSPANFEVYTAVLNPHDRIMGLDLPHGG
          NE.IDELEILCQERALA.F.LDGKQWG.NVQPL.GSPANFEVYTAVLNPHDRIMGLDLPHGG
Retrocopy NEYIDELEILCQERALATFSLDGKQWGINVQPLPGSPANFEVYTAVLNPHDRIMGLDLPHGG

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_40 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
Solanum tuberosum	PGSC0003DMG400029389	1 retrocopy	retro_stub_40 ,
Vitis vinifera	VIT_04s0008g00770	1 retrocopy	retro_vvin_49,