RetrogeneDB ID: retro_ptri_18

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 4:1946519..1946882(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0004s02890
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0017s11850
• Aliases: None
• Description: None

Sequence

>retro_ptri_18
AGAGGATCCCAACTTTTGGTCCACCCCAAACGTCACAGCTACGCCACAAAATCTAACCAACACCGTGTGGTCATAAGCCC
TTGTGGGAAATTGGTTTACCAAACCACCAAGAAGAGGGCTAGTGGACCCAAGTGCCCAGTTACTGGCAAGAGGATTCAAG
GGATCCCTCACTTGAGACCTGCTAAATACAAGAGGTCTAGACTGTCAAGGAATCGCAGGACTGTGAACCGTGCCTATGGT
GGAGTCTTGTCTGGAAGTGCTGTTAGGGAGAGAATTATCCGGGCTTTCTTGGTGGAGGAGCAAAAGATTGTGAAGAAGGT
TTTGAAGATTCAGAAGGCAAAGGAAAAACAGGCCTCAAAATGA

Alignment

ORF - retro_ptri_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 97.5 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRLTYRKRHSYATKSNQHRVVKTPGGKLVYQTTKKRASGPKCPVTGKRIQGIPHLRPAEYKRSRLSRNRR
          Q.L...KRHSYATKSNQHRVV..P.GKLVYQTTKKRASGPKCPVTGKRIQGIPHLRPA.YKRSRLSRNRR
Retrocopy QLLVHPKRHSYATKSNQHRVVISPCGKLVYQTTKKRASGPKCPVTGKRIQGIPHLRPAKYKRSRLSRNRR

Parental  TVNRAYGGVLSGSAVRERIIRAFLVEEQKIVKKVLKIQKAKEKQASK
          TVNRAYGGVLSGSAVRERIIRAFLVEEQKIVKKVLKIQKAKEKQASK
Retrocopy TVNRAYGGVLSGSAVRERIIRAFLVEEQKIVKKVLKIQKAKEKQASK

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_18 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_0017s11850	1 retrocopy	retro_ptri_18 ,