RetrogeneDB ID: retro_stub_44

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 6:57730675..57731368(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400030479
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400029753
• Aliases: None
• Description: None

Sequence

>retro_stub_44
ATGGATCTATCAAACCAACAAATTGTTGATTGTCCAAGCTTCAAGCTCGTAATCTTAGGCGATGGCGGTACTGGTAAAAC
AACTTTTCTCAAAAGGCATCTGAATGGTGAATTCGATAGAAAATACGAACCTACTATTAGTGTGGAGGTTCATCCATTAG
ACTTCTTCACGAATTACGGAAAAATTCGATTTAATTGTTGGGATACAGTTGGACAAGAGAATTTTGGAGGTGTTCGTGAT
AATTACTACATTCATGGCCAATGTGCAATTATCATGTTTGATTTTACAGTCCGCCTGAGCTACATGAATGTACCTACATG
GCATCGCGATCTTTTTAGGTTTTGTGAAAATGTCCCTTTTGTTCTTTGCGGAAACAAAATTGATATCAAACACAAACAGG
TTAAGGCGAAGGAGATTAACTTCTACCGGAGGAAGAAAAATTGGCCGTATTATGAGATCTCGGCGAAGAGTAATTATAAT
TTAGAGTTGCCTTTTTTATTCTTAGCTAGAAAGCTTGTTGGGGACGATAATCTTCATTTTGTGGAGTCGCCTGCACTTGC
TCCGCCGGAAGTGATTTTTGATTTAGATACGGAGAAATGGCGGGAAATAGAGTTTTTGAATTGCATTGGTAAACTGCCAC
TTCCGGATGAGGATGATGATTTAGCCGATGATCTACGCGGCTTTGATGAATAG

Alignment

ORF - retro_stub_44 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.18 %
• Parental protein coverage: 98.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALPNQQTVDYPSFKLVIVGDGGTGKTTFVKRHLTGEFEKKYEPTIGVEVHPLDFFTNCGKIRFYCWDTA
          M.L.NQQ.VD.PSFKLVI.GDGGTGKTTF.KRHL.GEF..KYEPTI.VEVHPLDFFTN.GKIRF.CWDT.
Retrocopy MDLSNQQIVDCPSFKLVILGDGGTGKTTFLKRHLNGEFDRKYEPTISVEVHPLDFFTNYGKIRFNCWDTV

Parental  GQEKFGGLRDGYYIHGQCAIIMFDVTARLTYKNVPTWHRDLCRVCENIPIVLCGNKVDVKNRQVKAKQVT
          GQE.FGG.RD.YYIHGQCAIIMFD.T.RL.Y.NVPTWHRDL.R.CEN.P.VLCGNK.D.K..QVKAK...
Retrocopy GQENFGGVRDNYYIHGQCAIIMFDFTVRLSYMNVPTWHRDLFRFCENVPFVLCGNKIDIKHKQVKAKEIN

Parental  FH-RKKNLQYYEISAKSNYNFEKPFLYLARKLAGDGNLHFVESPALAPPEVQIDLAAQALHEQELQQALN
          F..RKKN..YYEISAKSNYN.E.PFL.LARKL.GD.NLHFVESPALAPPEV..DL......E.E......
Retrocopy FYRRKKNWPYYEISAKSNYNLELPFLFLARKLVGDDNLHFVESPALAPPEVIFDLDTEKWREIEFLNCIG

Parental  Q-PLPDDDDE
          ..PLPD.DD.
Retrocopy KLPLPDEDDD

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_44 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	PGSC0003DMG400029753	1 retrocopy	retro_stub_44 ,
Triticum aestivum	Traes_1BL_7F667EEA3	1 retrocopy	retro_taes_6,