Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u42835.011

ChromosomeExonStartStopDirection
chr6H13489343434893364+
chr6H23489404234893848+
chr6H33489452534894361+
chr6H43489518734894927+
chr6H53489611534895891+
chr6H63489641434896192+
chr6H73489696534896755+


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
morexEMB0.00001331600.826652
morexETI00.2651480
morexLEA0.5501130.3820071.51226
morexEPI000
morexROO00.6016360.971512
morexROO200.000000146960
morexNOD000
morexRAC000
morexINF1000
morexINF204.979845.07593
morexCAR51.433120.4932762.27441
morexCAR152.662430.002897120
morexLEM0.00000000055781800
morexLOD000
morexPAL0.29405500.104399
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os02g03690.1 +3 0.0 717 337/387 (87%) protein|beta-amylase, putative, expressed
TAIR PP10 AT5G45300 @ ARAPORT
AT5G45300.1 @ TAIR		 +3 2e-176 510 240/381 (63%) Symbols: BMY2, BAM8 | beta-amylase 2 | chr5:18353636-18356696 FORWARD LENGTH=689
BRACH PP3 Bradi3g02800.1.p +3 0.0 747 352/389 (90%) pacid=32818286 transcript=Bradi3g02800.1 locus=Bradi3g02800 ID=Bradi3g02800.1.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 (1351 bp)

>BART1_0-u42835.011 1351 150831_barley_pseudomolecules
CTCAAAAGTATGAATGGTCTGGCTACAGGGACCTTTTTGGTATCATTAAAGAGTTCAAGC
TAAAAGTTCAGGTTGTGTTATCATTTCATGGGTCTGGGGAGTGTGGATCTGGTCCTGTGT
TAATTGCTCTTCCTAGGTGGGTAATGGAAATTGCACAAGAGAACCAAGATATATTTTTTA
CCGATCGAGAAGGTAGGAGGAATACAGAATGCCTCTCCTGGGGAATTGACAAAGAGCGTG
TCCTTCGAGGGAGAACTGGCATCGAGGTTTATTTTGATTTCATGAGGAGCTTTCATATGG
AATTCAGAACCCTATCTGAAGAGGGTCTTATTTCTGCTATTGAGATTGGATTGGGTGCTT
CTGGAGAGCTAAGATACCCTTCGTGTTCAGAAAAAATGGGCTGGAGATATCCTGGTATTG
GTGAGTTTCAGTGTTATGACAGGTATATGCAAAAGAACCTACGGCAATCAGCCTTGACAC
GGGGGCATTTGTTTTGGGCCCGTGGGCCTGATAATGCTGGCTACTATAATTCAAGGTCAC
ACGAGACTGGCTTTTTTTGTGACGGAGGTGATTATGACAGCTACTATGGGCGGTTCTTCC
TTAATTGGTATTCTGGAATCCTTATAGATCATGTGGATCAGGTGCTCTCACTTGCTACTC
TTGCATTTGATGGAGCAGCAGTTGTGGTGAAGATCCCCTCCATCTATTGGTGGTACAGAA
CTGCAAGCCATGCTGCAGAGCTTACTGCAGGATTCTACAACCCTACAAATCGAGATGGAT
ACTCTCCAGTTTTCAGAATGCTCAAGAAGCATTCCATAATTCTTAAAGTGGTTTGTTATG
GCCCAGAATTTACAGTTCAGGAGAATGATGAAGCACTTGCTGATCCAGAAGGTTTAACCT
GGCAGGTGAGAGATGTTGTTATGAACGCAGCATGGGATCATGGTCTATCTGTAAGTGTAG
AGAGTGCTCTTCCATGTCTTGACGTGGACATGTACTCTCGGATCCTTGACACAGCAAAGC
CGAGGAATGATCCTGACCGACACCATCTCTCATTCTTTGCATACCGTCAGCGAACTCCAT
TCCTTTTGCAGAGAGATGTGTGCTTCTCAGAGCTTGAGACCTTCGTAAAGTGTATGCACG
GGGAGGCTATCCAGAACTTTGTAGATTGAACTTGCTTTGGCGACGCATTCCCTGTTATGT
TGCAGCTCGCGTTCTGCAAATTTCCGGATTCCCTGCGTAGCTATCACAAGCTTTAACTCA
TATTGCTGATTGCTGCGTTCCGGCCATCCCCGCCTTTGCTATGGGTCAGCTAACCAGATG
GCACTGAAACTGTTGTGCTGGTGGTGGGCAA



Protein Sequence (388 aa)

>BART1_0-u42835.011 388 150831_barley_pseudomolecules
QKYEWSGYRDLFGIIKEFKLKVQVVLSFHGSGECGSGPVLIALPRWVMEIAQENQDIFFT
DREGRRNTECLSWGIDKERVLRGRTGIEVYFDFMRSFHMEFRTLSEEGLISAIEIGLGAS
GELRYPSCSEKMGWRYPGIGEFQCYDRYMQKNLRQSALTRGHLFWARGPDNAGYYNSRSH
ETGFFCDGGDYDSYYGRFFLNWYSGILIDHVDQVLSLATLAFDGAAVVVKIPSIYWWYRT
ASHAAELTAGFYNPTNRDGYSPVFRMLKKHSIILKVVCYGPEFTVQENDEALADPEGLTW
QVRDVVMNAAWDHGLSVSVESALPCLDVDMYSRILDTAKPRNDPDRHHLSFFAYRQRTPF
LLQRDVCFSELETFVKCMHGEAIQNFVD