RetrogeneDB ID: retro_ptri_4

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 10:15171023..15171350(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0010s16160
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0011s13810
• Aliases: None
• Description: None

Sequence

>retro_ptri_4
ATGGTGCTAGAATTCGAGATTCCTAGCGCTTTCGATCCATTTGCCGATGCCAAACAGTCAGGGACCAAAGAGTATGTGCA
CATACGCATACAGCAAAGGAATGGAAAGAAGAGCTTGACTACAGTTCAGGGTCTACCTAAAGAGTTGAGCTACGAAAAGA
TCCTCAAGACTCTCAAGAAAGATTTCTGTTGTAATGGGAATGTTGTGCAGGACAAGGAACTTGGCAAGGTCATTCAACTC
CAAGGTGATCAACGCAAGAACGTCCAGAATTTCCTTGTTAATCAGAACATTGTGAAGAAGGACCAGATCAAGATTCATGG
TTTTTGA

Alignment

ORF - retro_ptri_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.77 %
• Parental protein coverage: 94.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QTPSAYDPFADANAEDSGAGTKDYVHIRIQQRNGRKSLTTVQGLKKEFSYNKILKDLKKEFCCNGTVVQD
          ..PSA.DPFADA.......GTK.YVHIRIQQRNG.KSLTTVQGL.KE.SY.KILK.LKK.FCCNG.VVQD
Retrocopy EIPSAFDPFADAKQ----SGTKEYVHIRIQQRNGKKSLTTVQGLPKELSYEKILKTLKKDFCCNGNVVQD

Parental  PELGQVIQLQGDQRKNVSTFLVQAGIVKKESIKIHGF
          .ELG.VIQLQGDQRKNV..FLV...IVKK..IKIHGF
Retrocopy KELGKVIQLQGDQRKNVQNFLVNQNIVKKDQIKIHGF

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_4 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Populus trichocarpa	POPTR_0011s13810	1 retrocopy	retro_ptri_4 ,