RetrogeneDB ID: retro_stub_92

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:36094942..36095488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400016487
• Aliases: None
• Description: None

Sequence

>retro_stub_92
ATGATGAGTTTACTACTTGAGTCGTTCCCGATTGGGGTGACCAATTGGTGGTACGATATCAACAAGTCCATTCAATGGCA
ACATGGAATTTTCTTCACTCTTTGTGCTTTGTATTCTCTTGTTTCGATTATCGTGCTAATTCAAGTAATAAAGATCCATT
TAAGGATACCTTTATATGGTTGGTCAACACAAAAAGTGTTTCATATGATGAATTTTGTTGCAAATGGTGTTGGGGCAATC
GTATTTGGATTACATAACATATTTTTTATGTTACATCCAAACGTGCTTACGACTCGCGCGATTTTAGACCTACAAGGGTT
GTTTTTCTTTACAACATTTACCCACCTTGTTTGGTTTTGGGCTAATATATATTACAAAATTCAAAGTTTTCCTACGAGTA
AGCTCAAAATTTGGTATATTTCGATAAATTGTGTAATTTACTTGATTCAGGGTTGTATATGGATTTGTATCGAGATGAAT
GACAATGACGCAGTAGTACTAGTGAAATGGTTGTTCATTAGGAAGATATTTGTAGCAACTATACTG

Alignment

ORF - retro_stub_92 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.84 %
• Parental protein coverage: 64.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTRLPLGSSPIDIAGPATNWWDHVNESVQWQDGIFYSLCASYALVSAVALIQLIRIDLRVPEYGWTTQKV
          M..L.L.S.PI......TNWW...N.S.QWQ.GIF..LCA.Y.LVS...LIQ.I.I.LR.P.YGW.TQKV
Retrocopy MMSLLLESFPIGV----TNWWYDINKSIQWQHGIFFTLCALYSLVSIIVLIQVIKIHLRIPLYGWSTQKV

Parental  FHLMNFVVNGVRAIVFGFHKQVFLFHYKVLTL-AILDLPGLLFFSTFTLLVLFWAEIYHQARSLPTDKLR
          FH.MNFV.NGV.AIVFG.H...F..H..VLT..AILDL.GL.FF.TFT.LV.FWA.IY....S.PT.KL.
Retrocopy FHMMNFVANGVGAIVFGLHNIFFMLHPNVLTTRAILDLQGLFFFTTFTHLVWFWANIYYKIQSFPTSKLK

Parental  ISYIATNGAIYFIQACIWVYLWVNDNSTVEFIGKIFMAVVSVIAAL
          I.YI..N..IY.IQ.CIW.....NDN..V......F.....V...L
Retrocopy IWYISINCVIYLIQGCIWICIEMNDNDAVVLVKWLFIRKIFVATIL

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_92 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400016487	2 retrocopies	retro_stub_153, retro_stub_92 ,