RetrogeneDB ID: retro_stub_95

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 12:23603263..23603860(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG401008881
• Aliases: None
• Description: None

Sequence

>retro_stub_95
TCTGAGGCTAAAAGAGATGAGGAGTCTGCTACACATAATGGAGAAAATCATAAAGATGTGGAGTTGCAGAAGGAAATACG
TGGGAATTCTGATAAGGTACACAAAGTCACAATTCTTAATCTTCCTAAAGCGGTTGTTGAACCTTCAAGTGAAAAGCAAA
CCATCAATGAGGCAAAAGGTTTTCGGCCTCCTGAAGCTAGTTCACCCACAAGAAATCACCCAGAAGAACCATATGATCTC
CGCTCTACTGGTTTGCATTTGTGTAAGCCAATATTGCCTTGGCTAAATGGTGATGGTACTACAAATGAACGTGTCTACAA
GGGTCTTGTACGCCGTGTTCTTGGCATAGTGATGCAAAATCTGGGAATAAAAGAGGGTGATATTATCTGCCACATGCATG
TTCTGAATCCTCAGAGTTGCAGAAGTTTGTTAAACATGATGGTCCTGGATAACGTTATCTTTGTGGGTAAGATTCCTCAG
GCAAATCCAAGCGGAGCACCAGCAATTCTGAGTAGTCTTATTGGTAGCCATTTCAAGAAATCGAAGTTAATTTCAAGGGA
ACATTTCTTTGCAAACCCCTCTAGTACACACCTGTTG

Alignment

ORF - retro_stub_95 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 65.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SSPYEDCEAKTYEESATHNGENHKDVELQNSDKVHKVTILNLPKAVAEPSSKKQTINEAKGCRPTEASSP
          S....D.E..T.........E..K.....NSDKVHKVTILNLPKAV.EPSS.KQTINEAKG.RP.EASSP
Retrocopy SEAKRDEESATHNGENHKDVELQKEIR-GNSDKVHKVTILNLPKAVVEPSSEKQTINEAKGFRPPEASSP

Parental  TRNHPEEPYDIRSTGLHLCKPILPWLNGDGTTNERVYKGLVRRVLGIVMQNPGIKEGDIICHMHVLNPQS
          TRNHPEEPYD.RSTGLHLCKPILPWLNGDGTTNERVYKGLVRRVLGIVMQN.GIKEGDIICHMHVLNPQS
Retrocopy TRNHPEEPYDLRSTGLHLCKPILPWLNGDGTTNERVYKGLVRRVLGIVMQNLGIKEGDIICHMHVLNPQS

Parental  CRSLLNMMILDNVIFSRKIPQANPSGEPAILSSLIGSHFKKSKLVSREHFFANPSSTHLL
          CRSLLNMM.LDNVIF..KIPQANPSG.PAILSSLIGSHFKKSKL.SREHFFANPSSTHLL
Retrocopy CRSLLNMMVLDNVIFVGKIPQANPSGAPAILSSLIGSHFKKSKLISREHFFANPSSTHLL

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_95 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	PGSC0003DMG401008881	1 retrocopy	retro_stub_95 ,