RetrogeneDB ID: retro_stub_98

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 2:8801262..8801759(+)
• Located in intron of: PGSC0003DMG400002324

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400015000
• Aliases: None
• Description: None

Sequence

>retro_stub_98
GTGAATAACAGTGGTTTTACAAGCGGAAACAGTGATGGAAGGCCTAGAAGTTTTGACTCGGAGGCTAGAAAGAAATGCTG
GTCCAAAGCAGAGAAGGTTCCAGGTCGAGATCCCGAGAGGTGGAGAAAAGATGCAGCTGGCAACATTATTGGCAAGCGAT
TCCACAGCTGCCAAGGTTGCCTCTGCTTTGAGTATGATCACATTGTTCCCTTCTCTAAAGGTGGTGATTCAGTGTCAGAT
AATTGTCAAATTCTTCAAACAAGGGTTAATAGATCTAAAGCAGACAAGGTTGCAGTTGACACAAGACATTTGAAAGGATA
TTCTTGTGACATCAACTTCAGCGACAATGACCTTGACAAGATTGAGATGGCTGTTTATGGGGATATTAAGCGGTCAGACA
ATCAATGCCGTGTTCCAACAATAGATGAAATAATGGGGAAATACAAGTCTAAGAACGGCATTGCTAGCTGCAACTCCCAA
TAAAATATAAAAGCTTG

Alignment

ORF - retro_stub_98 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.28 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSSSSSPTRSQGERPRTFDGEAKRMCWAKAETVPGRHPERWRKDSAGNILCKRLFNCQGCLCFEYDHIIP
          ...S.........RPR.FD.EA...CW.KAE.VPGR.PERWRKD.AGNI..KR...CQGCLCFEYDHI.P
Retrocopy VNNSGFTSGNSDGRPRSFDSEARKKCWSKAEKVPGRDPERWRKDAAGNIIGKRFHSCQGCLCFEYDHIVP

Parental  FSKGGESIAENCQILQTRVNRLKSNKDEIDISRLKSYSCDIKFTDKELDVIEMAVYGDVLRPGKQCRCRT
          FSKGG.S...NCQILQTRVNR.K..K...D...LK.YSCDI.F.D..LD.IEMAVYGD..R...QCR..T
Retrocopy FSKGGDSVSDNCQILQTRVNRSKADKVAVDTRHLKGYSCDINFSDNDLDKIEMAVYGDIKRSDNQCRVPT

Parental  VAEVLGQYKSKDRAAPC-KLPYANESL
          ..E..G.YKSK...A.C..LP....SL
Retrocopy IDEIMGKYKSKNGIASC<QLPIKYKSL

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_98 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	PGSC0003DMG400015000	1 retrocopy	retro_stub_98 ,
Solanum lycopersicum	Solyc12g036250.1	1 retrocopy	retro_slyc_67,