RetrogeneDB ID: retro_ptri_37

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 5:9209704..9210141(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0001s40270
• Aliases: None
• Description: None

Sequence

>retro_ptri_37
ATGGATTCATCAAAAGATCACGAGAACTTTATTTACATTGTTAAGCTCGTTGAGCAAGTTGAATAATACAATGAAATGGC
AGATACAATGAAAAAAATAACAAATTTTAATGTTAAATAAATAGTAAAGGATAAACACTTACTATTTATGAGTTACAAGA
ATGTGACTGGTACGAGGAGGGAATCATGAGAATCCTCTCATTAATTAAGCAAAAATAGGAGTCGAAAGGGAATGAAACCA
ATGTTAAAAGGATAAAATAGTATAGGAATAAGGTGGAAGTAGAGCTAATCAATATTTGTAATGATATTATAGCTATAACT
GATAAGCATCTTATTCCATTATTTATAGCTAGAAAATCCTTTTCGTTTTACTATAAGATGAAATGTGATTATTATTAGTA
TATAGTAGAATTCAAGAGCGGTAATTAGAGGAAAGAG

Alignment

ORF - retro_ptri_37 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.54 %
• Parental protein coverage: 52.9 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MDSSKDRENFVYVAKLAEQAERYDEMVDAMKKVAKLDVELTVEERNLLSVGYKNVIGARRAS-WRILSSI
          MDSSKD.ENF.Y..KL.EQ.E.Y.EM.D.M.......V...V....LL...YKNV.G.RR.S..RILS.I
Retrocopy MDSSKDHENFIYIVKLVEQVE*YNEMADTMXXXTNFNVK*IVKDKHLLFMSYKNVTGTRRES<MRILSLI

Parental  EQKEESKGNETNVKRIKEYRQKVEAELTGICHDIMTVIDEHLIPSCTAGESTVFYYKMKGDYYRYLAEFK
          .QK.ESKGNETNVKRIK.YR.KVE.EL..IC.DI....D.HLIP...A..S..FYYKMK.DYY.Y..EFK
Retrocopy KQK*ESKGNETNVKRIK*YRNKVEVELINICNDIIAITDKHLIPLFIARKSFSFYYKMKCDYY*YIVEFK

Parental  SGNERKE
          SGN.RKE
Retrocopy SGN*RKE

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_37 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Populus trichocarpa	POPTR_0001s40270	3 retrocopies	retro_ptri_21, retro_ptri_37 , retro_ptri_38,
Populus trichocarpa	POPTR_0011s11210	1 retrocopy	retro_ptri_11,