RetrogeneDB ID: retro_stub_143

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 8:36967090..36967672(+)
• Located in intron of: PGSC0003DMG400013829

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400029922
• Aliases: None
• Description: None

Sequence

>retro_stub_143
GATATCTCAAACTCAGCAAAGCCTTCTGCCCTACAAGCATCAAAGACGAATATTTCCGTGAATCTGATTTCTATTGGGAA
AGATCTTATTGCCTCTAGAAACAAATTTGGTGCAGGAAGAAAAGATAACTATTCTGAAGCTCTGGAGAAAAAGGATGGCA
GGCAAGCACTAGCTGATCTTACAAACTCAAGCAAATAGCCGTTTGTTGCAGAAGAGCAATTTCTCCATAATCATCAGAAT
TGCATCAAAGCACAGAGAAAGGCCATGAACATGAGTTGTTTTCTGAAGGAAGTTGGATTAGATCATGATGATGTCCCCGT
GCAAATTGGAGAATCTCCACATGCACTTAAACCATCAATGAAGTCGAAGTCATCAGCATATCATCCAGAAAGCCCAACGC
ATTATGTCGAAGTGGAAGAGATGCCAGAACTGATTTTTTATGATCAGATTCATAGATATGAGGAAAATCGGGCTTGTGTA
TCTTTTTCCCCTTGTGATGCATCTCCTAAATCAGCAAAGCCACCATAAATCATCTGGACAGACGACGGTATTCTAGATTT
TGCATTGATTGGAACGCCTATC

Alignment

ORF - retro_stub_143 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.33 %
• Parental protein coverage: 71.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DISNSAKPSALQASKKNNSINRISIGKDHDASRKKFSAGTKANYSKGLEKKGGRKALADLTNSSKSSSVA
          DISNSAKPSALQASK.N.S.N.ISIGKD..ASR.KF.AG.K.NYS..LEKK.GR.ALADLTNSSK...VA
Retrocopy DISNSAKPSALQASKTNISVNLISIGKDLIASRNKFGAGRKDNYSEALEKKDGRQALADLTNSSK*PFVA

Parental  KDQFLHNHQNCVKAQRKVMDMSCFLKEIGLDHDDVPVHLGASPHALKPSMKSKSSTYQPDSPMKHYAEVE
          ..QFLHNHQNC.KAQRK.M.MSCFLKE.GLDHDDVPV..G.SPHALKPSMKSKSS.Y.P.SP..HY.EVE
Retrocopy EEQFLHNHQNCIKAQRKAMNMSCFLKEVGLDHDDVPVQIGESPHALKPSMKSKSSAYHPESP-THYVEVE

Parental  EMPELMFYDEVRRCEQNRACASCPPCVASPKSRY---VSWMDDSVLDFALIGTPI
          EMPEL.FYD...R.E.NRAC.S..PC.ASPKS.......W.DD..LDFALIGTPI
Retrocopy EMPELIFYDQIHRYEENRACVSFSPCDASPKSAKPP*IIWTDDGILDFALIGTPI

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_143 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	PGSC0003DMG400029922	1 retrocopy	retro_stub_143 ,