RetrogeneDB ID: retro_stub_16

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 9:13526065..13526818(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400013063
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400006066
• Aliases: None
• Description: None

Sequence

>retro_stub_16
ATGTACTTTGCGAGCTTGAGCTACACTTCTCCGACTCTTCTTGCCTCGATGGTCAACACTATAGCTGCCTTATCATTTGT
ACTAGCAGTTATTCTCAGGTTGGAAGATGCTTACATTCGAAATCCTAGAGGAATAGCAAAAGTCCTAGGAACCTTGGTTT
CCTTGGCTGGGGTTATGAGCATGACATTATACAAAGGACCTGTTGTGAAAAGCTTAGGACATCCTCTCATCTACATTCAC
AGAGGGAATGGTGTTGTCCACGAGAACTGGTCAAAAGGCATGATCCTCACTGCTGTTAGCTGCATTACGTGGTCAATATG
GTACATCATGCAGGCTTACACTTTGAAAAGATATCCAACACAACTATCACTGACTACATGGATGAGTTTTGTTGGTGCAG
CACAATCAGCTTTCTATACAGTAATTGTACAACACAAACGAACAGCTTGGACCATGGGTTTCAACATTGATTTCTGGTCT
ACTCTGTATGGGGGCATAGTGATGTCTGGTTTAGTAGTGTACATACAACTCTGGTGCATTGAACAAAAGGGACCAGTTTT
CGTAACTATGTTCAACCCACTCTCAACCGTATTAGTTGCAGTTCTAGCATATTTCGTCCTTGGTGAAAAGCTCTACACGG
GCAGCATCATTGGAGCAGTAATTATCATTATTGGACTGTACTTGCTTTTGTGGGGTAAAGAAGATCCACAACCAGAATTG
AAAGAGAGAGAAAGAGCAATGCTACATAACTAA

Alignment

ORF - retro_stub_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 82.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYFVSLNYTSPTLLASMVNTIAALTFVLAVILRLEDANIRNPRGIAKVVGTLVSLAGVMSMTLYKGPVVK
          MYF.SL.YTSPTLLASMVNTIAAL.FVLAVILRLEDA.IRNPRGIAKV.GTLVSLAGVMSMTLYKGPVVK
Retrocopy MYFASLSYTSPTLLASMVNTIAALSFVLAVILRLEDAYIRNPRGIAKVLGTLVSLAGVMSMTLYKGPVVK

Parental  SLGHPLIYIHRGNGVVHENWSKGLILTAASCITWSIWYIMQAYTLKRYPAQLSLTTWMSFVGAAQSAFYT
          SLGHPLIYIHRGNGVVHENWSKG.ILTA.SCITWSIWYIMQAYTLKRYP.QLSLTTWMSFVGAAQSAFYT
Retrocopy SLGHPLIYIHRGNGVVHENWSKGMILTAVSCITWSIWYIMQAYTLKRYPTQLSLTTWMSFVGAAQSAFYT

Parental  VIVQHKRAAWTMGFNIDFWSTLYGGIVMSGLVVYIQLWCTEQKGPVFITVFNPLSTVLVAVLAYFVLGEK
          VIVQHKR.AWTMGFNIDFWSTLYGGIVMSGLVVYIQLWC.EQKGPVF.T.FNPLSTVLVAVLAYFVLGEK
Retrocopy VIVQHKRTAWTMGFNIDFWSTLYGGIVMSGLVVYIQLWCIEQKGPVFVTMFNPLSTVLVAVLAYFVLGEK

Parental  LYTGSIIGAVIVIIGLYLLLWGKEDPQPEMKNEDPMM
          LYTGSIIGAVI.IIGLYLLLWGKEDPQPE.K.....M
Retrocopy LYTGSIIGAVIIIIGLYLLLWGKEDPQPELKERERAM

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_16 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400006066	1 retrocopy	retro_stub_16 ,