RetrogeneDB ID: retro_stub_41

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:41664764..41665082(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400024414
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

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

Sequence

>retro_stub_41
ATGAAAACCCTAAACTTTTTCCCTAAGTACAAAGCCATCAAGATGTTCCTTGTGAGGAACATTGTTGAACAAGTTGATGT
ACGTGATATTAAGAAAGCTTGTGCTTTTGAATTGTACACTCTTCCTAAGCTCTATTTGAAGATGCAGTACTGTGTTTCAT
GTGCAATTCACTCCAAGGTTGTTAGAGTCTGTTCTCGTACTGATAGGAGAGTTCGTGAGCCTCCACAGCGTTACAGGCGC
CCAAGGGATGATCTCGCAAAGACAGGACATCCACGCCCTGTTGGAGGACCCCCCTGCTGCTCCACGCACTTAAGTTAG

Alignment

ORF - retro_stub_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.87 %
• Parental protein coverage: 72.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PKDKAIKRFLVRNIVEQAAVRDVQEACAFELYTLPKLYLKMQYCVSCAIHSKVVRVRSRTDRRVREPPQR
          PK.KAIK.FLVRNIVEQ..VRD...ACAFELYTLPKLYLKMQYCVSCAIHSKVVRV.SRTDRRVREPPQR
Retrocopy PKYKAIKMFLVRNIVEQVDVRDIKKACAFELYTLPKLYLKMQYCVSCAIHSKVVRVCSRTDRRVREPPQR

Parental  FRRPRDDLPKTGQAPRPAGGPP
          .RRPRDDL.KTG..PRP.GGPP
Retrocopy YRRPRDDLAKTGH-PRPVGGPP

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_41 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 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,