Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u29974.010

ChromosomeExonStartStopDirection
chr4H1511456072511455921+
chr4H2511457260511457229+
chr4H3511457495511457384+
chr4H4511457741511457592+
chr4H5511457957511457873+
chr4H6511458147511458084+
chr4H7511459293511458273+


grey: non-coding, green: Barley Morex IBSC 2017 Transcript CDS, red: Barley RTD exons



Salmon TPM Values: sixteensamplesmorex

These TPM values were generated by using the RNA-seq data from a 16-tissue experiment in Morex (published here) were calculated using Salmon (version Salmon-0.8.2) using BaRTv1.0-QUASI as the reference transcript dataset. Click here for more information about the RNA-seq experiment and materials


SampleTreatmentRep 1Rep 2Rep 3
morexEMB6.6973513.205115.2575
morexETI33.348327.012712.037
morexLEA75.176371.963884.8516
morexEPI14.379143.23127.4368
morexROO57.197724.669115.35
morexROO2000.0862017
morexNOD59.449109.33826.948
morexRAC11.44034.08776.67994
morexINF11.531874.18516.89657
morexINF230.64224.098731.5253
morexCAR522.533620.08913.80128
morexCAR1522.924719.702521.7467
morexLEM54.647567.800822.4479
morexLOD24.42497.2393565.2257
morexPAL31.229329.459733.8121
morexSEN44.5101102.52482.8692



Homology to Model Species (BLASTX to E-value < 1e-30)

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os03g15890.2 +3 1e-43 159 71/82 (87%) protein|RNA recognition motif containing protein, expressed
TAIR PP10 AT1G07350 @ ARAPORT
AT1G07350.2 @ TAIR		 +3 2e-34 126 56/89 (63%) Symbols: | RNA-binding (RRM/RBD/RNP motifs) family protein | chr1:2258816-2259586 REVERSE LENGTH=129
BRACH PP3 Bradi1g67145.1.p +3 2e-46 166 76/82 (93%) pacid=32805382 transcript=Bradi1g67145.1 locus=Bradi1g67145 ID=Bradi1g67145.1.v3.1 annot-version=v3.1




Barley PseudoMolecules GBrowse

Click here to see more tracks within GBrowse -->



grey: non-coding, green: Barley Morex IBSC 2017 Transcript CDS, red: Barley RTD exons



CDS Sequence (1616 bp)

>BART1_0-u29974.010 1616 150831_barley_pseudomolecules
CTTCCGGCAGGTCCTCTCTATTTATTCACACGAGCGCGCGTGCACCATCCAACGGGAAAA
GAGAGGCGGTGGTCGCAGGTCGGAACTGACGGAGGCAGAGGCGAAGACGAAGACAGAGAC
TCGAGAGGCCTCGCAGCGGCGACGAATCAAAGATGTCGTATTCGAGGTACAGGAGTCGTT
CAAGGAGTGTGGACTCGAGTGATGTTGAGAACCCTGGGAACAATCTCTTTGTGACTGGTT
TATCATCTCGTCTAACTGATCGAGATCTGGAGAAGCATTTCTCTACAGAGGGAGAGGTGA
TTGATGCAAGTATTGTACTTGATCCATGGACAAGGGAATCACGGGGATTTGGATTTGTTA
CCATGGCCAATCTTAAGGAGGCAGAACGCTGCATCAAATATCTCGACAGTTCAGTGCTGG
AAGGTCGTGTCATTACTGTTGAGAAGCAGCAGGTTGATGCCCGCAGCTGTATGGCATCAA
ATTCAAAAGATACACAACCTAAGATCGAAACAATGCTACCTCAACCAAAGGGCAAAGAGA
AGACGAGGTCGAACCCCAACACCGGGAAGGTACCTTGGCAGCAAATCATCGCGTCGAAGG
AGGTATTCCCGAAGCAGGTCACCTGTTAGGAGAGACCGTTACGGCTCACGCTACCCGCCC
GAGCTAGAACGTTCTTATTCTCCTTATCGCAGAGGACGATCATACTCTCGTCATGACAGG
CATAGATCATACTCCCCCTATGGAAGGAGGCCATCCTACTCCCCCTATGAAAGGAGGCCA
TCCTACTCTCCCTATGGCAGAAGGAGATCATACTCTCCTTCCGACAGGTCGGAGTCTCCC
TACCACAGGCGTAGATCCTACTCACCCTACGACAGGCGTCACTCACCCCGCTATGGTCAT
CGCCACCGTTCAAGATCCCCATACAGTTACAGAAGGCGGAGGTCATGCTCCCATGACCGT
TATGTTTCAGCATACTACAGCAGGCGCTATTCTCCAAGGAACAGAAGACGGAGTTACTCT
CGCAGCGTATCACCACGCAGGAGCTACTCCCGTAGCTGCTCCCTGGCGTCAGAAGAATCA
AGGAGCTGTTCTCCGCAGAAAGGATATGCTGAAAGCAAGGCATCGCGCAGCAGGTCACCT
GCGATTGCGAAGAGGCGTTCTAGAGAAAGCTATGCGCACAGCCGCAGTTCATGCTCGAGG
TCCGTCTCCAGGGAGCGCTCAACCTCATCAAGCACCTGATGGTTTACAAAGTGCCTTGAT
GACTTTGGATGTTTGTAAACAATGTGGATGGTATGATCGTGTACCTAGTGAAGCAGCTGT
ATTTCGTCATCGTTAACATCTTAAATTGCAGTCTGCTTCCATACTATAGGAGAAAAATGC
AGAAAATTTCCTACAGATTGCCTATTCCACAAGGATTTTATAGCATACTTCTACAACGGA
AAAAACGCAGAAATTTTCATAAATATTGGCGAGGTCATTTCTTTGTTTCAGATGACCCAG
TGCGGATTTTTCTATAGGAATTCGATACTGCAATTTTCCTTTGTTTATAAGATCTCTAAC
TCAAACCTCATTTTATTATTCTTTGACAAGTTGAATACACTTTCACTGTATTTACC



Protein Sequence (158 aa)

>BART1_0-u29974.010 158 150831_barley_pseudomolecules
MSYSRYRSRSRSVDSSDVENPGNNLFVTGLSSRLTDRDLEKHFSTEGEVIDASIVLDPWT
RESRGFGFVTMANLKEAERCIKYLDSSVLEGRVITVEKQQVDARSCMASNSKDTQPKIET
MLPQPKGKEKTRSNPNTGKVPWQQIIASKEVFPKQVTC