RetrogeneDB ID: retro_stub_54

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 1:69199480..69200299(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400042273
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400025377
• Aliases: None
• Description: None

Sequence

>retro_stub_54
ATGGGGAGCCAAATTGCTGTCCCTGTGAAAGAAACCTTCTTCATATCACATGGTTCCCCAATGCTTTCAATAGATGATTC
CTTACCTGCCAGACATTTCTTGAAATGCTTCAAACAGAAAGTCTTCACCCAGAAACCCAATTCAATTTTGGTGATCTCTG
GTCATTGGGAGACTTCAGAGCCTACTGTGAATTGCATCAATGGCCTCAATGACACTATTTACGACTTCTACGGCTTCCCA
GAACAGATGTACCAGCTGAAATATCAAGCACCAGGAGCTCCAAAATTAGCCAAAAGAGTGAAGGAACTGCTCAAGTCATC
TGGTTTCAATCGAGTGCACGAAGACAATAACCGAGGCCTAGATCATGGTGCATGGGTGCCTCTTATGCTCATGTATCCAG
AGTCTGACATCCCAGTCTGCCAGCTTTCTGTCCAGACAAAGAAGGATGGAACTCATCATTTTAACATTGGGAAAGCATTA
GCCCCTCTCAAGGAAGAGGGTGTCCTCATAGTTGGTTCTGGATCTGCAACTCACAACTTGAGGGCTTTGCGCGATACGGC
TGGCGTCGCTTCTTGGGCTATGGATTTTGACAATTGGCTTAAGGAATCCCTTGTTAATGGAAGGTATGAAGATGTCAACA
ACTATATGACAAAAGCACCTTGTGCCAAAATTGCACACCCATGGCCTGACCACCTGTATCCATTACATGTAGCAATGGGT
GCAGCAGGTGAAAATGCCAAAGCTGAACTTATTCATCATAGCTGGAGCAGCCATGCTCTTTCTTACGCCTCCTACAAGTT
TAAGTCACAGCCTAAGTAG

Alignment

ORF - retro_stub_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.48 %
• Parental protein coverage: 96.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPVKETFFISHGSPTLSIDESLPARTFLKSFKERFMINQKPNSILVISAHWETSEPTVNSIRGRQDTIHD
          .PVKETFFISHGSP.LSID.SLPAR.FLK.FK......QKPNSILVIS.HWETSEPTVN.I.G..DTI.D
Retrocopy VPVKETFFISHGSPMLSIDDSLPARHFLKCFKQK-VFTQKPNSILVISGHWETSEPTVNCINGLNDTIYD

Parental  FYGFPKSMYQLKYPAPGSPELAKRVKDVLMASGFPIVHEDKKRGLDHGAWVPLMLMYPEADIPVCQLSVQ
          FYGFP..MYQLKY.APG.P.LAKRVK..L..SGF..VHED..RGLDHGAWVPLMLMYPE.DIPVCQLSVQ
Retrocopy FYGFPEQMYQLKYQAPGAPKLAKRVKELLKSSGFNRVHEDNNRGLDHGAWVPLMLMYPESDIPVCQLSVQ

Parental  PNRDGTYHYNLGKALASLKDEGVLIIGSGSATHNLRALGPSKNVSSWALEFDNWLKDALLSGRHQDVNNY
          ...DGT.H.N.GKALA.LK.EGVLI.GSGSATHNLRAL.....V.SWA..FDNWLK..L..GR..DVNNY
Retrocopy TKKDGTHHFNIGKALAPLKEEGVLIVGSGSATHNLRALRDTAGVASWAMDFDNWLKESLVNGRYEDVNNY

Parental  DMKAPHAKVAHPWPEHIYPLHVALGAAGEGVNGELIHHSWDLGALSYASYRFPS
          ..KAP.AK.AHPWP.H.YPLHVA.GAAGE....ELIHHSW...ALSYASY.F.S
Retrocopy MTKAPCAKIAHPWPDHLYPLHVAMGAAGENAKAELIHHSWSSHALSYASYKFKS

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_54 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400025377	1 retrocopy	retro_stub_54 ,
Solanum lycopersicum	Solyc11g072550.1	1 retrocopy	retro_slyc_2,