RetrogeneDB ID: retro_stub_15

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 6:2798577..2799129(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400020568
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400015423
• Aliases: None
• Description: None

Sequence

>retro_stub_15
ATGATTAATTTAATCAAAGTTAGAGAAAAACAAAAAGAAGCTGCTGAAAATGCAGGATCAAAAACAGCAATTAAAGAACA
AACAGCGTCAAAATTACGTGTTCATAGAGATATTAGTGAATTAACTTTACCACCAATTTGTAAAATTGAATTTCCAAATG
GAAAAGATGATCTTATGAATTTTGAAGTTGCAATTAAACCTGATGAAGGTTATTATCATGATGGTGAATTTCCATTTACA
TTTGAAATTCCAATACTTTATCCACACGATGCACCAAAAGTTAAGTGCAAAATCAAAGTTTATCATCCAAATATTGATTA
TGATGGAAATGTTTGTCTTAATATTCTTAGAGAAGATTGGAAACCTGTTTTGAATATTAATGCTGTTATTTATGGTTTGG
TTCATTTGTTTACTGAACCCAATCATGAAGATCCACTTAATCCTGAAGCAGCTGATGAATTAAGAGATAATCCCATATCG
TTTGAATCCAACGTTAGGAGTGCTATGTGGGGAGAAACTGTGCATGGCTTGACTTATGATCGTATCCTATAA

Alignment

ORF - retro_stub_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.07 %
• Parental protein coverage: 97.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MIKLFKVKEKQRELAENANGKPPIKKQSAGELRLHKDISELNLPKTCSISFPNGKDDLMNFEVTIRPDDG
          MI.L.KV.EKQ.E.AENA..K..IK.Q.A..LR.H.DISEL.LP..C.I.FPNGKDDLMNFEV.I.PD.G
Retrocopy MINLIKVREKQKEAAENAGSKTAIKEQTASKLRVHRDISELTLPPICKIEFPNGKDDLMNFEVAIKPDEG

Parental  YYMGGTFVFSFSISSIYPHEAPKVKCKTKVYHPNIDLEGNVCLNILREDWKPVLNINTVIYGLYHLFTEP
          YY..G.F.F.F.I...YPH.APKVKCK.KVYHPNID..GNVCLNILREDWKPVLNIN.VIYGL.HLFTEP
Retrocopy YYHDGEFPFTFEIPILYPHDAPKVKCKIKVYHPNIDYDGNVCLNILREDWKPVLNINAVIYGLVHLFTEP

Parental  NHEDPLNHEAAAVLSDNPSMFESNVRRAMSGGYV-GQTY
          NHEDPLN.EAA..L.DNP..FESNVR.AM.G..V.G.TY
Retrocopy NHEDPLNPEAADELRDNPISFESNVRSAMWGETVHGLTY

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_15 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400015423	1 retrocopy	retro_stub_15 ,