RetrogeneDB ID: retro_stub_43

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 4:48765724..48766123(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400016932
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400012453
• Aliases: None
• Description: None

Sequence

>retro_stub_43
ATGTATAATTGTAGGCCGAAGTGTGATCGGAAGGGCAAAATATTGAAGCACGAGTATCAATCAAAGCAACTTCCGTCAAC
GAGGATACAACCAGATCCCCGATGGTTCATCAATACTCGGGTGATTAGTCAGGAGAAATTGGAATCCTTTAGAGAAGAGA
TCCAGGATCGGCTTTCTAGCAACTACAATATCATAATGAATGGAAGTAATTTTCCCATGTCCCTTGTGAATGAGCACAAG
AAGAAAGGAAAAGCTCATCAACTTGGCAGTAAGCCTTCTGCTGGAACAGAGAATAAACACGCAAAATATTTTAAATCATT
TTTCCAAGATGATTCGAGGGAGAAGCCGAAGATAAGATTGGATAACTCAGATTTTAGTAAATTAGTAGATACTACTTAA

Alignment

ORF - retro_stub_43 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.34 %
• Parental protein coverage: 92.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MYNCRPKRDRKGKILKHKYQSKQLPSTRIQPDPRWFINTRVISQEKLESFREEIQDRLSSNYNIIMNGSN
          MYNCRPK.DRKGKILKH.YQSKQLPSTRIQPDPRWFINTRVISQEKLESFREEIQDRLSSNYNIIMNGSN
Retrocopy MYNCRPKCDRKGKILKHEYQSKQLPSTRIQPDPRWFINTRVISQEKLESFREEIQDRLSSNYNIIMNGSN

Parental  LPMSLVNERKKKGKAHQLGSKPSAGTEKKHAKHFKS
          .PMSLVNE.KKKGKAHQLGSKPSAGTE.KHAK.FKS
Retrocopy FPMSLVNEHKKKGKAHQLGSKPSAGTENKHAKYFKS

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_43 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400012453	1 retrocopy	retro_stub_43 ,
Solanum lycopersicum	Solyc07g063280.1	2 retrocopies	retro_slyc_92, retro_slyc_98,