RetrogeneDB ID: retro_ptri_12

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 13:10266356..10267013(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0013s10250
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0018s09030
• Aliases: None
• Description: None

Sequence

>retro_ptri_12
ATGGCCGCCTCGTTCTCGATTTCCAGACTCATCCTCTCCTCTCCAACCCAAATATCCACCACCGCCGCCACCGCCAAATC
TTTCCTCTCATCTCTCCCCCTCAAACCCAACCGCCTACCCAAGCCCCTGAGAACCACCACCAGAAAATTCTCCACTATCT
CCGCCACCATTTCTGTCGGGGACAAACTCCCAGAAGCCACCCTCTCCTACTTTGACTCCGAAGGAGAGCTCCAAACCACC
ACAATCTCCTCCCTAACATCCGGGAAAAAATCAATCCTTTTCGCTGTCCCGGGCGCCTTCACCCCAACATGCTCCCAGAA
ACACCTTCCAGGTTTCGTGGAGAAATCGGCAGAGCTAAAGTCAAAAGGGGTAGACACAATCGCGTGTATATCAGTGAACG
ACGCGTTTGTGATGAAAGCATGGAAGGAGGATTTGGGGATAAAAGATGATGGAGTGCTGCTTTTGTCTGATGGGAATGGG
GATTTTACAAAGGCAATAGGGTGTGAGTTGGATTTGAGTGACAAGCCAGTTGGGCTAGGAGTGAGGTCAAGGAGGTATGC
GTTGTTGGCTGAAGATGGGGTTGTCAAGGTTCTTAATTTGGAGGAAGGTGGAGCTTTTACTTCCAGTGGAGCTGAGGATA
TGCTCAAGGCTCTCTGA

Alignment

ORF - retro_ptri_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.93 %
• Parental protein coverage: 99.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  APIAVGDVLPDGKLAYFDEQDQLQEVSVHSLVAGKKVILFGVPGAFTPTCSLKHVPGFIEKAGELKSKGV
          A.I.VGD.LP...L.YFD....LQ.....SL..GKK.ILF.VPGAFTPTCS.KH.PGF.EK..ELKSKGV
Retrocopy ATISVGDKLPEATLSYFDSEGELQTTTISSLTSGKKSILFAVPGAFTPTCSQKHLPGFVEKSAELKSKGV

Parental  TEILCISVNDPFVMKAWAKSYP-ENKHVKFLADGSATYTHALGLELDLQEK--GLGTRSRRFALLVDDLK
          ..I.CISVND.FVMKAW..........V..L.DG....T.A.G.ELDL..K..GLG.RSRR.ALL..D..
Retrocopy DTIACISVNDAFVMKAWKEDLGIKDDGVLLLSDGNGDFTKAIGCELDLSDKPVGLGVRSRRYALLAEDGV

Parental  VKAANIEGGGEFTVSSADDILKDL
          VK..N.E.GG.FT.S.A.D.LK.L
Retrocopy VKVLNLEEGGAFTSSGAEDMLKAL

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_12 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 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT1G65980	1 retrocopy	retro_atha_13,
Arabidopsis lyrata	fgenesh2_kg.2__836__AT1G65980.1	1 retrocopy	retro_alyr_5,
Glycine max	GLYMA07G09240	1 retrocopy	retro_gmax_12,
Hordeum vulgare	MLOC_12954	1 retrocopy	retro_hvul_9,
Populus trichocarpa	POPTR_0018s09030	1 retrocopy	retro_ptri_12 ,
Prunus persica	PRUPE_ppa012586mg	1 retrocopy	retro_pper_22,
Sorghum bicolor	Sb03g030950	1 retrocopy	retro_sbic_22,
Selaginella moellendorffii	SELMODRAFT_159225	1 retrocopy	retro_smoe_4,
Solanum lycopersicum	Solyc07g020860.2	1 retrocopy	retro_slyc_41,
Theobroma cacao	TCM_028816	1 retrocopy	retro_tcac_8,