RetrogeneDB ID: retro_stub_55

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 9:2868247..2868751(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400008958
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG401023527
• Aliases: None
• Description: None

Sequence

>retro_stub_55
ATGGCTTCTTCACAAGCCGCTCTTCTCCTCCAAAAACAGCTCAAAGACCTAAACCGTCATCCGGTCGACGGCTTCTCCGC
CGGTTTAGTCGATGAGAACAACGTTTTTGAATGGAGTATCTCAATCATCGGTCCACCGGAAACTTTATTCGACGGCGGAT
TTTTCAACGCTACAATGAGTTTTCCGACGGATTACCCTAACAATCCACCGACGGTGAAATTCACAACGGAGATCTGGCAT
CCGAATGTTTATTCTGACGGTAGGGTTTGTATATCGATTCTTCATCCACCAGGTGATGATCCGAATCATTATGAGCTGGC
GAGTGAGCGGTGGACGCCGGTGCATACGGTGGAGAGTATTATGCTGAGTATAATTTCGATGCTTACCAGTCCGAATGATG
AATCGCCGGCGAATGTTGATGCTGCTAAGGAATGGAGGGATAATAGGGCGGAATTTGTGAAGAAGGTGAAGAGATGCGTG
AGGAAATCACAAGAGATGTTGTGA

Alignment

ORF - retro_stub_55 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.34 %
• Parental protein coverage: 98.81 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SASQASLLLQKQLKDLCKKPVDGFSAGLVDEINLFEWSVTIIGPPETLYDGGFFNAIMSFPQNYPNSPPT
          ..SQA.LLLQKQLKDL...PVDGFSAGLVDE.N.FEWS..IIGPPETL.DGGFFNA.MSFP..YPN.PPT
Retrocopy ASSQAALLLQKQLKDLNRHPVDGFSAGLVDENNVFEWSISIIGPPETLFDGGFFNATMSFPTDYPNNPPT

Parental  VKFTSEIWHPNVYSDGKVCISILHPPGDDPNGYELASERWSPVHTVESIMLSIISMLSSPNDESPANVEA
          VKFT.EIWHPNVYSDG.VCISILHPPGDDPN.YELASERW.PVHTVESIMLSIISML.SPNDESPANV.A
Retrocopy VKFTTEIWHPNVYSDGRVCISILHPPGDDPNHYELASERWTPVHTVESIMLSIISMLTSPNDESPANVDA

Parental  AKEWRDNRDEFKKKVSRCVRRSQEMM
          AKEWRDNR.EF.KKV.RCVR.SQEM.
Retrocopy AKEWRDNRAEFVKKVKRCVRKSQEML

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_55 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	PGSC0003DMG401023527	1 retrocopy	retro_stub_55 ,
Solanum lycopersicum	Solyc05g054550.2	1 retrocopy	retro_slyc_23,