RetrogeneDB ID: retro_stub_110

Retrocopy location

• Organism: Potato (Solanum tuberosum)
• Coordinates: 4:4255956..4256478(+)
• 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_110
AACAAGTCTGATAATTATGTTACTTTCAAGGAAAAGACAATAAATCCAAAGAAATATTATGTAAAGCCCAACACTGGAAT
TTTCATGCCTCAGTCTTCCAACGACATCATAATTACAATGCAATGGCATAAAGACGCTCTACTATACATGCAATGCAAGG
ATAAATTCCTGCTTCAAAGTGTTGTTGCAGGCCCTTGAACTACTGCAAAGTACATTACTCCCGAGATGTTCCATAAGGAG
TCGGGGAATTATGTGGAGGACTGCAAGTTGAAAGTTGTTTATGTTCCTCCTCAAGTGCCACTACATGTAAGGCAGGGGTC
CGAGGAAGGTTCTTCTCCTACGGCTTTAGTATTCAAAATTTGAACTGTAAATATATCGGAGCATAATAATATATCAAGGT
CGTATAATGAGCAACAAGACAACTCGTTGGAGACAAAGGCACTAATTTCAAAGCTGACAGATGAGAAAATTTTTGTTATG
CAGCAAAATGAAAAGCTTCAGCAAGAATTGGAACTCTTGAGA

Alignment

ORF - retro_stub_110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.0 %
• Parental protein coverage: 73.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NKSDDYVAFKVKTTNPKKYCVRPNTGIVMPRSTCEVIVTMQAQKEAPPDMQCKDKFLLQSVIVSPGTMAK
          NKSD.YV.FK.KT.NPKKY.V.PNTGI.MP.S....I.TMQ..K.A...MQCKDKFLLQSV...P.T.AK
Retrocopy NKSDNYVTFKEKTINPKKYYVKPNTGIFMPQSSNDIIITMQWHKDALLYMQCKDKFLLQSVVAGP*TTAK

Parental  DITPEMFNKESGNHVEEVKLRVAYVPPQPPPSPVREGSEEGSSPRASI----SENGAEFHNASRTYAEPQ
          .ITPEMF.KESGN.VE..KL.V.YVPPQ..P..VR.GSEEGSSP.A........N..E..N.SR.Y.E.Q
Retrocopy YITPEMFHKESGNYVEDCKLKVVYVPPQ-VPLHVRQGSEEGSSPTALVFKI*TVNISEHNNISRSYNEQQ

Parental  DNSSETKALILKLSEEKKSAIQQNNKLKQELELLR
          DNS.ETKALI.KL..EK....QQN.KL.QELELLR
Retrocopy DNSLETKALISKLTDEKIFVMQQNEKLQQELELLR

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_110 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,