RetrogeneDB ID: retro_stub_88

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:41500439..41500819(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400020566
• Aliases: None
• Description: None

Sequence

>retro_stub_88
ATGACATTCAAGCGAAGGAACGAAGGTCGTAACAAACATGGACATGACCATATCAAGTTGATCCGCTGCTCTAACTGCGG
CAAATGCTGCCCTAAGGACAAAGCCATCAAGAGGTTCCTTGTGAGGAACATTGTTGAACAAACTGTTGTACGTGATGTTC
AGGAAGCTTGTGCTTTTGAATTGTACACTCTTCCTAAGATCTATTTGAAGATGCAGTACTGTGTTTGATGTGCAATTCAC
TCCAAGGTAGTTAGAGTCCATTCTCGTACTTTAGGAGAGTTCGTGAGCCTCCACAGCGTTTCAGGTGCCCAAGGAATGAT
CTCCCAAAGACAGGACAAGCTCCACCCCCTGCTGGAGGACCCCCTGCTGCTCCACGCACT

Alignment

ORF - retro_stub_88 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTFKRRNGGRNKHGRGHVKFIRCSNCGKCCPKDKAIKRFLVRNIVEQAAVRDVQEACAFELYTLPKLYLK
          MTFKRRN.GRNKHG..H.K.IRCSNCGKCCPKDKAIKRFLVRNIVEQ..VRDVQEACAFELYTLPK.YLK
Retrocopy MTFKRRNEGRNKHGHDHIKLIRCSNCGKCCPKDKAIKRFLVRNIVEQTVVRDVQEACAFELYTLPKIYLK

Parental  MQYCVSCAIHSKVVRVRSRT-DRRVREPPQRFRRPRDDLPKTGQAPRPAGGPPAAPRT
          MQYCV.CAIHSKVVRV.SRT..RRVREPPQRFR.PR.DLPKTGQAP.PAGGPPAAPRT
Retrocopy MQYCV*CAIHSKVVRVHSRT<FRRVREPPQRFRCPRNDLPKTGQAPPPAGGPPAAPRT

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_88 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Brassica oleracea	Bo8g090770	1 retrocopy	retro_bole_5,
Solanum tuberosum	PGSC0003DMG400020566	2 retrocopies	retro_stub_41, retro_stub_88 ,
Solanum tuberosum	PGSC0003DMG400025305	1 retrocopy	retro_stub_30,
Solanum lycopersicum	Solyc06g007470.2	1 retrocopy	retro_slyc_57,