RetrogeneDB ID: retro_stub_90

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:54775488..54776118(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400019920
• Aliases: None
• Description: None

Sequence

>retro_stub_90
ACGAGAAATCATTCATTGGCAAAACAAACAGTACTTGAATATGGTATCGTGGTTGAATACGTCCCTGGAGGCACTCTTAG
ATCACACCTCTTAAAAAATCATATAAAAAAGTTGCCATTGATTTATGTAATTCAACTAGCATTAGATGTTGCAAGAGGGT
TGAGTTATCTTCACTCTAAGAAAATTGTTCATAGAGATGTAAAGAGTAGTAATTTAGTTGTGGATAAGGAAGGAAGAGTA
AAAATAATTGACTTTGGAGTATCTCGAATCGAGGCTTCATGTCCTACTAACATGACTGCGCAAACTGGGACTATTGGTTA
CATGGCTCCTGAGGTTCTTATTGGGTTACCATATGATCATAAATGTGATGTTTATAGTTTTGGAATTTGTTTGTGGGAGA
TATATTGTTGTTCAATTCCATATATTGGACAAATTTGTCCTTCTCATGAAATATGTCCAAATGTGTACAAGAGTCTAACG
CCTGAAATACCTAACACTTGTCCAAGTGCTGTGGCCAATATAATGAAACAATGTTGGAATGAAAATCCAAAAAAGAGGCC
AGAGATGAAGGAAGTGGTGCTCATGTTGGAAGCCATTGACACAACTCAAGATGCACAAAAAGGTTGTTTT

Alignment

ORF - retro_stub_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 59.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SRYRSLEKQPSLEYGIVVEYVPGGTLRSHLLKNHIKKLPLNSVIQLALDVARGLSYLHSKKIVHRDVKTS
          .R..SL.KQ..LEYGIVVEYVPGGTLRSHLLKNHIKKLPL..VIQLALDVARGLSYLHSKKIVHRDVK.S
Retrocopy TRNHSLAKQTVLEYGIVVEYVPGGTLRSHLLKNHIKKLPLIYVIQLALDVARGLSYLHSKKIVHRDVKSS

Parental  NLVMDKDGRVKIIDFGVSRIEASCPLDMTAQIGTIGYMAPEVLIGLPYDHKCDVYSFGICLWEIYCCSIP
          NLV.DK.GRVKIIDFGVSRIEASCP..MTAQ.GTIGYMAPEVLIGLPYDHKCDVYSFGICLWEIYCCSIP
Retrocopy NLVVDKEGRVKIIDFGVSRIEASCPTNMTAQTGTIGYMAPEVLIGLPYDHKCDVYSFGICLWEIYCCSIP

Parental  YNGKI-PSSHTSPCIYKSLRPEIPNKCPSVVANIMKQCWHADPKERPEMKEVVLMLEAIDTSQVAEKGCF
          Y.G.I.PS....P..YKSL.PEIPN.CPS.VANIMKQCW...PK.RPEMKEVVLMLEAIDT.Q.A.KGCF
Retrocopy YIGQICPSHEICPNVYKSLTPEIPNTCPSAVANIMKQCWNENPKKRPEMKEVVLMLEAIDTTQDAQKGCF

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_90 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400019920	1 retrocopy	retro_stub_90 ,