RetrogeneDB ID: retro_ptri_38

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 5:13005228..13005702(-)
• 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_38
GATTCATCAAAAGATTATAAGAACTTCATCTATGTTACTAGTCTCATTGAGCAAGCTAGACACTAGAATGAAATGGTGGA
TGCAATGAAAAAAGTGACAAAGCTTGATATTGAATTAACAGTGGAAGAGAGAAACTTAATTTTTATGGGTTACAAGAATG
TAATTGGTGATATGAGAAAATCATGGAGAGTCTTGTCATTAATTGAGTGGAAGAAAATGTAGAAAGAGAATGAGAAAATT
GAACAGGATCAAAGAGTATAGGAAGAAGTGGAAAAAGATTTAACTGACATTTGTCATGATATTATGATTGTGATTGACGA
GCATCTTATTTTATCATTTATAGCTGATAAATTCTTTGTGTTTTACTATAGAACAAAAGGTTATTATTACCAATAATTAA
CATAATTCAAGAGTTAAAATAAGAGGAAAGAGGTAGCTAATTGATTACTTAAAACATATATGACTACTACAACA

Alignment

ORF - retro_ptri_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.75 %
• Parental protein coverage: 57.82 %
• Number of stop codons detected: 7
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DSSKDRENFVYVAKLAEQAERYDEMVDAMKKVAKLDVELTVEERNLLSVGYKNVIGARRASWRILSSIEQ
          DSSKD..NF.YV..L.EQA....EMVDAMKKV.KLD.ELTVEERNL...GYKNVIG..R.SWR.LS.IE.
Retrocopy DSSKDYKNFIYVTSLIEQARH*NEMVDAMKKVTKLDIELTVEERNLIFMGYKNVIGDMRKSWRVLSLIEW

Parental  KEESKGNETNVKRIKEYRQKVEAELTGICHDIMTVIDEHLIPSCTAGESTVFYYKMKGDYYRYLAEFKSG
          K...K.NE............VE..LT.ICHDIM.VIDEHLI.S..A....VFYY..KG.YY..L..FKS.
Retrocopy KKM*KENE-KIEQDQRV*EEVEKDLTDICHDIMIVIDEHLILSFIADKFFVFYYRTKGYYYQ*LT*FKS*

Parental  NERKEAADQSLKAYETATT
          N.RKE.A...LK.Y.T.TT
Retrocopy NKRKEVAN*LLKTYMTTTT

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_38 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 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,