RetrogeneDB ID: retro_ptri_17

Retrocopy location

• Organism: Western balsam poplar (Populus trichocarpa)
• Coordinates: 13:2018246..2019065(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: POPTR_0013s03280
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: POPTR_0018s06860
• Aliases: None
• Description: None

Sequence

>retro_ptri_17
ATGGCTCTCCCTCCGTCTGCCCAAAACCCAGTTGTTGAGCAGCAGAAAGTTACAATATCAAACAAACATGGTGAAAAACT
GATAGGCTTATTACATGACACTGGATCCAACGACATAGTTATATTATGCCATGGTTTTTGTTCCACAAAGGAAAACGATA
TCATGGTGAATCTTGCCAAGGCATTAGAAAAGGAAGGAATCTCTGCCTTCCGTTTCGACTTGGCTGGAAACGGGGAAAGT
GAAGGTTCATTTGCATATGGTAATTACAGGAGAGAGGCTGATGATTTACGTGCTGTAATCGAACACTTCCGCGGAGCAAG
CCCAAGCAGGGGCATAAGTGCAATTCTTGGGCATAGTAAAGGAGGCGATGTGGTGCTCCTATATGCTTCAAAATATCAGG
ATATCAGCACAGTTTTCAATGTTTCTGGCCGTTATGATCTGAAGAGAGGCATTGAAGAACGAACTGGAAAGGGTTTTATG
GAAAAGATCAAACAAGATGGATTCATTGATGTTAAGGATGGAACGGGGAGTGTCATTTATCGTGTGACCAAGGAAAGTCT
GATGGATCGCCTGAATACTGATATGCATGAAGCATGTCTTGCGATCAAGAAGGATTGCAGGGTCTTCACCATTCATGGTT
CTGCTGATGAAATCATCCCAGTGGAGGATGCGTTAGAGTTTGCCAAGATCATACCAAATCACAATCTACACATCATAGAA
GGAGCAAATCATTGCTACACTTCACATCTAACTGAGTTAGCATCTGTTGTGTCGAACCTCATGAAAGCAACCTTAAAGCA
GGGCAAGGATACCCCTTAG

Alignment

ORF - retro_ptri_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.52 %
• Parental protein coverage: 84.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MALPPSGQNPVVEQQKVIISNKHGEKLVGLLHDTGSNEIVILCHGFRSTKGNDTMVNLAKALEKEGTSSF
          MALPPS.QNPVVEQQKV.ISNKHGEKL.GLLHDTGSN.IVILCHGF.STK.ND.MVNLAKALEKEG.S.F
Retrocopy MALPPSAQNPVVEQQKVTISNKHGEKLIGLLHDTGSNDIVILCHGFCSTKENDIMVNLAKALEKEGISAF

Parental  RFDFAGNGESEGSFAYGSYWREADDLRSVMEHFRGAS--RAISAILGHSKGGDVVLLYASKYQDITTVFN
          RFD.AGNGESEGSFAYG.Y.READDLR.V.EHFRGAS..R.ISAILGHSKGGDVVLLYASKYQDI.TVFN
Retrocopy RFDLAGNGESEGSFAYGNYRREADDLRAVIEHFRGASPSRGISAILGHSKGGDVVLLYASKYQDISTVFN

Parental  VSGRYDLKRGIEERIGKDFMEKIKQDGFINVKNRTGSVIYRVTEESLMDRLNTDIHKACLVINKECRVFT
          VSGRYDLKRGIEER.GK.FMEKIKQDGFI.VK..TGSVIYRVT.ESLMDRLNTD.H.ACL.I.K.CRVFT
Retrocopy VSGRYDLKRGIEERTGKGFMEKIKQDGFIDVKDGTGSVIYRVTKESLMDRLNTDMHEACLAIKKDCRVFT

Parental  IHGSADEIIPVEDALEFAKIIPNHSLHIIEGANHSYTSHQTELAAVVLKLMKATLQQ
          IHGSADEIIPVEDALEFAKIIPNH.LHIIEGANH.YTSH.TELA.VV..LMKATL.Q
Retrocopy IHGSADEIIPVEDALEFAKIIPNHNLHIIEGANHCYTSHLTELASVVSNLMKATLKQ

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_17 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT3G47590	1 retrocopy	retro_atha_5,
Oryza sativa indica	BGIOSGA001352	1 retrocopy	retro_oind_81,
Brassica oleracea	Bo3g134660	1 retrocopy	retro_bole_24,
Brassica rapa	Bra019508	1 retrocopy	retro_brap_47,
Hordeum vulgare	MLOC_20645	1 retrocopy	retro_hvul_20,
Oryza sativa japonica	OS01G0579900	1 retrocopy	retro_osat_70,
Populus trichocarpa	POPTR_0018s06860	1 retrocopy	retro_ptri_17 ,