RetrogeneDB ID: retro_stub_156

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 9:47601363..47601716(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400028781
• Aliases: None
• Description: None

Sequence

>retro_stub_156
CTACGTTTGGAGTATCGACACACACCCATAGCTATTCTTAAAAAGTCTAAGCAGCTGATCCATTGAAGCGAAGCAAAGTA
CATTATTGCCACCAGTTTGATAGTGAGACATCTCAAGAGAGATTTAGCTACTCAACGACTCCACAATAGATTTCTTTCAT
TTGTTCATGATGCCATATTGGAGGACTTGATTGTTACAACATAGATTGTTAGGAAGCATACTTGGTATCGCGTTGATGGC
TCCAAGATAATGAAGGATTACTTGACCCCAAGGAACTAAACAACACCAAGTATAAGTTGGAGACCTTTTCAATAGTTTAC
AAAGAGCTTTCAGGTAAAGATATTGTGCTTAAG

Alignment

ORF - retro_stub_156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.78 %
• Parental protein coverage: 61.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRKAFRKVHVRLVRELEKKFSGKDVIFI-ATRRIVRPPKRGSAAQRPRTRTLTSVHDAILEDLVVPAEIV
          LR...R.....................I.AT..IVR..KR..A.QR...R.L..VHDAILEDL.V...IV
Retrocopy LRLEYRHTPIAILKKSKQLIH*SEAKYIIATSLIVRHLKRDLATQRLHNRFLSFVHDAILEDLIVTT*IV

Parental  GKRTRYRVDGSKIMKVY-LDPKERNNTEYKLETFSAVYRKLSGKDVVFE
          .K.T.YRVDGSKIMK.Y.LDPKE.NNT.YKLETFS.VY..LSGKD.V..
Retrocopy RKHTWYRVDGSKIMKDY<LDPKELNNTKYKLETFSIVYKELSGKDIVLK

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_156 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400028781	1 retrocopy	retro_stub_156 ,
Solanum lycopersicum	Solyc06g069090.2	1 retrocopy	retro_slyc_101,