RetrogeneDB ID: retro_stub_104

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 3:28368729..28369084(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400000965
• Aliases: None
• Description: None

Sequence

>retro_stub_104
GCGTATGCGACGATGAAGTTGACAGAACAAAGGCTAGAGGGGTTCAATAGAAGATTGATTAGGATTACTCTTTCTACCAA
AAACGTTAAGAGTCTTGAGAAAATGTGTACGGATTTGGTCTGAGGTGCTAAGGACAAGAGATTAGAGTAAAGGGACTTGT
AGAAATGCCAACAAAGGTTCTTAACATTATCCCTAGGAAATCTTCCTATGGAGAAGGCACAAATACGTGGGACAAGTTTG
AGCTGGGGGTTCACGAGTGCGGATTGACCTTTTTAGCTCCCCAATTATTGTCAATCAAATCACCTCAATCACCATTGAGC
CTGGTGTCGAGGTTGATGTCACCATTGTTGATTCC

Alignment

ORF - retro_stub_104 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.92 %
• Parental protein coverage: 99.18 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AYAAMKPTKPGLEEPQEQVHKIRITLSSKNVKNLEKVCADLVRGAKDKRL-KVKGPVRMPTKVLNITTRK
          AYA.MK.T...LE........IRITLS.KNVK.LEK.C.DLV.GAKDKRL..VKG.V.MPTKVLNI..RK
Retrocopy AYATMKLTEQRLEGFNRRL--IRITLSTKNVKSLEKMCTDLV*GAKDKRL<RVKGLVEMPTKVLNIIPRK

Parental  SPCGEGTNTWDRFELRVH-KRVIDLFSSPDVVKQITSITIEPGVEVEVTIADS
          S..GEGTNTWD.FEL.VH....IDLFSSP..V.QITSITIEPGVEV.VTI.DS
Retrocopy SSYGEGTNTWDKFELGVH<RVRIDLFSSPIIVNQITSITIEPGVEVDVTIVDS

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_104 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 3 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400000965	3 retrocopies	retro_stub_104 , retro_stub_108, retro_stub_65,
Solanum tuberosum	PGSC0003DMG400003291	1 retrocopy	retro_stub_105,
Physcomitrella patens	PP1S257_105V6	1 retrocopy	retro_ppat_38,