RetrogeneDB ID: retro_stub_18

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 8:50385989..50386523(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400001840
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400026509
• Aliases: None
• Description: None

Sequence

>retro_stub_18
ATGGAATTGAATGCTAACGTGTCCACAAAAAGGACAATAAACCCTAGGAAGACGGATATCGGAGGTAAACCCTTTATACT
CATCATTTGTGGCAGCCTCGTTTACTACCACTGTGCCTATCGGAATTCTAGTCTCGTCTCTCTCATCTCAGACGTCTTTA
TTGTACTCCTTTGTTCCCTCGCCATTCTCGGACTCCTCTTTCGCCAGATGAACATCTCGGTACCTGTGGATCCTCTTGAG
TGGCAGATCTCTCAGGACGCTGCCAACATGTTTTTTGCCTGCCTCGCCAATACTATCGGTGCTGCTGAGTCTGTTCTACG
GGTTGCTGCTACTGGCCATGATAAGCGCTTGTTCCTTAAGGTTGTGGCTGCTCTGTATGTTCTATCATCTCTTGGAAGGA
TAGCATCGGGTGTTACCATTGCCTATGCTGGACTCTGCTTTCTTTGCCTTTACATGCTCGCTGAGAACTTGCAATTGATT
AGCTCGAGGTATCCAAGGAGAAGAGACGGCACGAACACAGTTCAGGACGACTAA

Alignment

ORF - retro_stub_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.25 %
• Parental protein coverage: 88.52 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLNANEEIRRTINPRRKKDLRGPVPFILIICGTLVYYHCVYRNASIVSLVSDVFIVIICSLAILGLLYRQ
          .LNAN....RTINPR.K.D..G..PFILIICG.LVYYHC.YRN.S.VSL.SDVFIV..CSLAILGLL.RQ
Retrocopy ELNANVSTKRTINPR-KTDIGGK-PFILIICGSLVYYHCAYRNSSLVSLISDVFIVLLCSLAILGLLFRQ

Parental  MNISVPVDPLEWQISQNTANRVLACIANTIGAAESVLRVSATGHDKRLFVKVVVTLYVLSVLGRIASGVT
          MNISVPVDPLEWQISQ..AN...AC.ANTIGAAESVLRV.ATGHDKRLF.KVV..LYVLS.LGRIASGVT
Retrocopy MNISVPVDPLEWQISQDAANMFFACLANTIGAAESVLRVAATGHDKRLFLKVVAALYVLSSLGRIASGVT

Parental  VAYAGLCFLCLYMLAENSQLIS
          .AYAGLCFLCLYMLAEN.QLIS
Retrocopy IAYAGLCFLCLYMLAENLQLIS

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_18 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	PGSC0003DMG400026509	1 retrocopy	retro_stub_18 ,