RetrogeneDB ID: retro_ptri_5

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 2:10205486..10205735(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0002s13770
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0014s12370
• Aliases: None
• Description: None

Sequence

>retro_ptri_5
ATGCGTTGGCCAGTGGAGGAAGATGCCACAGGCAGGAAGGAGGAGGACTTCAGCACTGGGCCACACTCTGTTCTAATGAT
GAGCGTCAGAGAAAACACCCAGGGGCTGATTAACTTGCGTAATAAGAGGCAGCTTCTTGCACATATGAGGGCATTCGATC
TACTCTACGACATGGTTTTGGAGAATATTAGGGGGATGTGGACTGTGGAACGGAAAACTGGTAAAGGCAAGGAGAGCTCG
AGCACTTAA

Alignment

ORF - retro_ptri_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.49 %
• Parental protein coverage: 75. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSRPMEEDAPSKNEEEEFSTGPLSVLMMSVKNNTQVLINCRNNKKLLGRVRAFDRHCNMVLENVREMWTE
          M..P.EEDA.....EE.FSTGP.SVLMMSV..NTQ.LIN.RN...LL...RAFD....MVLEN.R.MWT.
Retrocopy MRWPVEEDATGR-KEEDFSTGPHSVLMMSVRENTQGLINLRNKRQLLAHMRAFDLLYDMVLENIRGMWTV

Parental  VPKTGKGKKKA
          ..KTGKGK...
Retrocopy ERKTGKGKESS

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_5 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Populus trichocarpa	POPTR_0014s12370	1 retrocopy	retro_ptri_5 ,