RetrogeneDB ID: retro_ptri_8

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 2:17878340..17879066(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0002s21410
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0013s05030
• Aliases: None
• Description: None

Sequence

>retro_ptri_8
ATGGGAGCAATCAAGGGAGCCATAGTAGATGGGATTTTGACAGCCATGTGGGTATTCAGCGTTCCTTTGCTGGGTGTTTT
CTCCTCCATCATAGCAACATATGTGGGTGTTGAGGCCATGTCAATAGCAGGTCTTTTCATATCCATTAATGTCGCCGCTC
TTTTTATGCTAACTTTCAGCTTGATAGGAGCTGCCTTCGGTGGTGCCAGTTTCAACCCTGCCACGACGATAACACTCTAC
ATAGCTGGCCTAAAGCCTGATGCATCTCTCTTGTCCATGGCTTTGCGTTTTCCTGTTCAGGCAGCTGGTGGGGTTGGTGG
TGCCATGGCAATTAGGGGAGTGATGCCAAAACATTACAGGCATGTGCTCAAAGGAGGTCCTTCTTTGAGGGTGGACTTGC
ATACAGGGGCGATTGCTGAGGGGGTGTTGACTTTTCTGATCTGTCTTACTTTACATTTTCTTTTGCTCAAGGGCCCTAAA
AATGTTGTGTTGAAGGTGTGGTTGCTAGCGGTGGCTACTGTGGGATTGGTCATGGCTGGAGGTAAGTATACCGGCCCTTC
AATGAATCCTGCCAACGCTTATGGATGGGCTTATTTGGGCAATAGGCATACCACCTGGGATTTCTTCTATGTCTATTGGA
TTTGCCCCTTTATAGGGGCAATTTTAGCTGCTTTTGTTTCTAAATTTCTTTTCAAGGCAGCACCGATCAAGGAGAAAAAA
GCCTGA

Alignment

ORF - retro_ptri_8 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.25 %
• Parental protein coverage: 99.58 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGAVKAAIGDAVFTFMWVFVSSMFGLFTNVIVTALGLQTLVWAPVLANASLIFAFVFLFNFLGEFLGGAT
          MGA.K.AI.D...T.MWVF.....G.F...I.T..G......A...........F...F...G...GGA.
Retrocopy MGAIKGAIVDGILTAMWVFSVPLLGVFSSIIATYVGVEAMSIAGLFISINVAALFMLTFSLIGAAFGGAS

Parental  FNPTGTASFYAAGVGGD-SLFSMALRFPAQAAGSVGGSLAILEVMPVQYKHML-GGPTLQVDLQTGGLAE
          FNP..T...Y.AG...D.SL.SMALRFP.QAAG.VGG..AI..VMP..Y.H.L.GGP.L.VDL.TG..AE
Retrocopy FNPATTITLYIAGLKPDASLLSMALRFPVQAAGGVGGAMAIRGVMPKHYRHVLKGGPSLRVDLHTGAIAE

Parental  GVLTFLMTFAVLVIILKGPRSSLVQAWFLATVTVTLVSAGSTYTGPSMNPAFAFGWAYVNKWHNTWEQLY
          GVLTFL.........LKGP.......W.LA..TV.LV.AG..YTGPSMNPA.A.GWAY....H.TW...Y
Retrocopy GVLTFLICLTLHFLLLKGPKNVVLKVWLLAVATVGLVMAGGKYTGPSMNPANAYGWAYLGNRHTTWDFFY

Parental  VYWICPFIGAILAAWVFRVVFPPPAPKQKK
          VYWICPFIGAILAA.V....F.....K.KK
Retrocopy VYWICPFIGAILAAFVSKFLFKAAPIKEKK

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_8 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Medicago truncatula	MTR_7g085070	1 retrocopy	retro_mtru_16,
Populus trichocarpa	POPTR_0013s05030	1 retrocopy	retro_ptri_8 ,
Prunus persica	PRUPE_ppa010591mg	1 retrocopy	retro_pper_47,
Theobroma cacao	TCM_026035	1 retrocopy	retro_tcac_30,