RetrogeneDB ID: retro_ptri_39

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 6:11672352..11672860(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0002s21490
• Aliases: None
• Description: None

Sequence

>retro_ptri_39
CTAAGAGTTGCTAACATGGACACAAAGAAACTAGCATGAGTGACATTTAAGCATAAATTACATTAATATTTGCACTATTA
AAATCCTTGCCTTGAAAAACGTATCAGAAGATTCTCATAAGACATCCTGGACTATCCTTTACACTCCAATGAGCTCTTTG
AAGTTCTAAAGACATTGGTTGACCTTATTGAGACAACTATATGAGCTATTTACATTGATAGTAGTTTCTCGATTAATATT
ATATGAAAGATATTTAAAGGTTTGTTGGAATCAATGATTAGCCTAAAAAAATCTGAAAGTACATCCTATGATAGAGTTGT
ACAAAATACACTAGAAAAAAATTTCAAAAGTAAAATTTATGGATTCATGGAAAGAAAACATAAATATAGAGGTCCTCGTT
GATGGTCAACTTGTGGGCAAAGGTATTTATTGTCCAAAGAAGAAAATTACACATAATATGGCAACCAAGGATACATTAGG
GAATATCAGGAAAGTCTTTGGAGACAAA

Alignment

ORF - retro_ptri_39 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.71 %
• Parental protein coverage: 58.89 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LRSANVDTEKLARVAIKHKLHRYLRHKMPLLEEQIREFSQAILDYPLHSNGLVETPKALADIVEAAIGAV
          LR.AN.DT.KLA.V..KHKLH.YL....P.LE..IR.FS..ILDYPLHSN.L.E..K.L.D..E..I.A.
Retrocopy LRVANMDTKKLA*VTFKHKLH*YLHY*NPCLEKRIRRFS*DILDYPLHSNELFEVLKTLVDLIETTI*AI

Parental  FIDSNFSIDVVWKIFKDLLEPIIS-QETLKVHPVTELYEVCQKRNLKVKFVDLWKENMAFDVFIDDQFVG
          .IDS.FSI....KIFK.LLE..IS....LKVHP..ELY........KVKF.D.WKEN....V..D.Q.VG
Retrocopy YIDSSFSINII*KIFKGLLESMIS>XXXLKVHPMIELYKIH*XXXSKVKFMDSWKENINIEVLVDGQLVG

Parental  RGTYGLKKEIAHNRAAKNALNNIRKILSEK
          .G.Y..KK.I.HN.A.K..L.NIRK....K
Retrocopy KGIYCPKKKITHNMATKDTLGNIRKVFGDK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Populus trichocarpa was not studied using RNA-Seq expression data.

ChIP-Seq

Populus trichocarpa was not studied using ChIP-Seq data.

EST

Populus trichocarpa was not studied using EST data.

TSS

Populus trichocarpa was not studied using FANTOM5 data.

Lab

retro_ptri_39 was not experimentally validated.

Homology

Retrocopy orthology:

Populus trichocarpa 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
Populus trichocarpa	POPTR_0002s21490	3 retrocopies	retro_ptri_33, retro_ptri_39 , retro_ptri_40,