RetrogeneDB ID: retro_stub_7

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 10:45900880..45901711(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: PGSC0003DMG400026670
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400027984
• Aliases: None
• Description: None

Sequence

>retro_stub_7
ATGGCGGAGAAAATCACCGGAACGAACCCTAAAACCACCGTACACGGTGTTACAACCAACAACAATTTGGATACGAGAAA
TGCAGACAGACGTGTATGGTTGATGAAATGCCCTACCGTTGTCTCTCGATTCTTCGAACAGCATCAACACTCTACTTCCG
GTGAAACTGATCTCTCTTTTAATTCTCCGAGACCTGTTGCCAAAGTCACCGTCGTCGTTGATCCTCTAATCGCCAATGAT
TCAACTCAATTTACCATGGAATTAGCCGGAACTTCATCTGGAAACATGCCCACTCACTACTCCATGGATATGTCAACAGA
TTTTGTTCCAATGTCGATATTTTCTGAATCAGGTCAAGGAAGGGTTTCGGTCGAAGGAAAGATATATCACAAATTTGATA
TGAAGCCTCATCATGAAAACATTGAGAATTATGGAAAACTTTGTCGTGAGAGGACGAATAAGTACATGACGAAAAGTAGA
CAAATTCAGGTTATTGATAATGATAATGCTAAACATATGAGGCCTATGCCTGGATTTTTCGCAACTAAGGCTTCTGGATC
TGCTGCAGAGAAGAAGAAGGTGCCTAGTAAAGGATTAGAAATGAAAAGAACAAGGAGGGATCGTGACGAAATGGAAGAAA
TTATGTTCAAACTGTTTGAGAGGCAATCAAATTGGACGTTGAAACAGCTCGTCCATGAGACGGACCAGCCTGAGCAATTT
ATGAAAGACATGCTCAAACTACTCTGCATTTACAATAATAAGGGCGCTCATCAAGGCACTTATGAGCTGAAGCCGGAGTA
TAAGAGAACAGAAGACAAGACTGATTCTTGA

Alignment

ORF - retro_stub_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.55 %
• Parental protein coverage: 98.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEMGGNDVGNMPKSYSLNMFQDFVPMCVLSETGQGRVTMEGKVEHKFDMTPHTRNMEEYRKMCRERTNKS
          ME..G...GNMP..YS..M..DFVPM...SE.GQGRV..EGK..HKFDM.PH..N.E.Y.K.CRERTNK.
Retrocopy MELAGTSSGNMPTHYSMDMSTDFVPMSIFSESGQGRVSVEGKIYHKFDMKPHHENIENYGKLCRERTNKY

Parental  MIKNRQIQVIDNDRGVNMRPMPGMIGMIASSSKDKKKAVPVKGPEVKRTRRDRGELEDIMFKLFERQPNW
          M.K.RQIQVIDND....MRPMPG.....AS.S...KK.VP.KG.E.KRTRRDR.E.E.IMFKLFERQ.NW
Retrocopy MTKSRQIQVIDNDNAKHMRPMPGFFATKASGSAAEKKKVPSKGLEMKRTRRDRDEMEEIMFKLFERQSNW

Parental  TLKQLVQETDQPAQFLKEILNELCVYNKRGTNQGTYELKPEYKKSVEDT
          TLKQLV.ETDQP.QF.K..L..LC.YN..G..QGTYELKPEYK.....T
Retrocopy TLKQLVHETDQPEQFMKDMLKLLCIYNNKGAHQGTYELKPEYKRTEDKT

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_7 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400027984	1 retrocopy	retro_stub_7 ,
Solanum lycopersicum	Solyc07g032090.2	1 retrocopy	retro_slyc_44,