RetrogeneDB ID: retro_stub_96

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 12:31693186..31693627(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: PGSC0003DMG400026015
• Aliases: None
• Description: None

Sequence

>retro_stub_96
AAGCCCAACACTTGAATTGTCATGCCTAACTCTTTCAGCGATGTCATAATTAGAATGCAACCGCAGAAAGAGGCTCAACC
AGTCATGCAATGCAAGGATAAAATCTTGCTTCAAAGTGTTGTTGCAAGCCTTAGAACTACTGCAAAGGACATTACTCTCA
AGATGTTCATTAAGGAGTCGGGGAATTGTGTGGAGGACTGCAAGTTGAAAGTGATTTATGTTCCCCTCAAGTGCCACTGC
CTATAAGGGAGGGGTCTGAGGAAGGTTATTCTCCTAGGACTTTAGTATCCGAAAATAGAGCTGTAAATATATTCGAGCTT
AATAATATTTCAAGGTCATATAATGCGCAGCAAGACAACTCGTTGGACAAAGGCACTAATTTGAAAGCTGACAGAGGAGA
AAATTTCTATTATGCAGTAAAATAACAAGCTTCAGCAAGAA

Alignment

ORF - retro_stub_96 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.93 %
• Parental protein coverage: 61.97 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RPNTGIVMPRSTCEVIVTMQAQKEAPPDMQCKDKFLLQSVIVSPGTMAKDITPEMFNKESGNHVEEVKLR
          .PNT.IVMP.S...VI..MQ.QKEA.P.MQCKDK.LLQSV..S..T.AKDIT..MF.KESGN.VE..KL.
Retrocopy KPNT*IVMPNSFSDVIIRMQPQKEAQPVMQCKDKILLQSVVASLRTTAKDITLKMFIKESGNCVEDCKLK

Parental  VAYVP-PQPPPSPVREGSEEGSSPRASISENGA----EFHNASRTYAEPQDNSSETKALILK-LSEEKKS
          V.YVP.PQ.P..P.REGSEEG.SPR...SEN.A....E..N.SR.Y...QDNS...K...LK.L.EEK.S
Retrocopy VIYVP<PQVP-LPIREGSEEGYSPRTLVSENRAVNIFELNNISRSYNAQQDNSLD-KGTNLK>LTEEKIS

Parental  AIQQNNKLKQE
          ..Q.NNKL.QE
Retrocopy IMQ*NNKLQQE

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_96 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Solanum tuberosum	PGSC0003DMG400026015	3 retrocopies	retro_stub_106, retro_stub_110, retro_stub_96 ,