Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u29736.002

ChromosomeExonStartStopDirection
chr4H1483706263483705742+
chr4H2483706465483706392+
chr4H3483706600483706543+
chr4H4483706780483706679+
chr4H5483707382483707226+
chr4H6483712253483711561+


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
morexEMB27.957921.485530.9897
morexETI0.001900587.236780.00711249
morexLEA11.46739.0210610.8037
morexEPI0.09079220.02727660.00444827
morexROO14.236418.27346.86761
morexROO26.243362.63410.0608665
morexNOD51.89750.43898420.3501
morexRAC0.492030.04100370.560901
morexINF130.171416.901320.0314
morexINF211.576511.846820.7903
morexCAR535.853327.841532.6552
morexCAR157.201542.6416511.3642
morexLEM0.01802186.153715.80119
morexLOD0.1911620.1949153.03341
morexPAL0.1013640.1266411.41101
morexSEN0.0007492830.004568360.0468972



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os03g27320.3 +1 7e-147 425 264/310 (85%) protein|steroid binding protein, putative, expressed
TAIR PP10 AT5G58220 @ ARAPORT
AT5G58220.3 @ TAIR		 +1 2e-86 269 159/304 (52%) Symbols: TTL | transthyretin-like protein | chr5:23554546-23555861 REVERSE LENGTH=311
BRACH PP3 Bradi1g60700.3.p +1 4e-161 461 270/308 (88%) pacid=32804009 transcript=Bradi1g60700.3 locus=Bradi1g60700 ID=Bradi1g60700.3.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 (1606 bp)

>BART1_0-u29736.002 1606 150831_barley_pseudomolecules
TCTCAGTGATGCAGTAAAATATGGTCATCTCCATTGAAAATTACGAAAAAAAATTCGTTG
CAATGTACGGGCCTTTTGTTAGTAAGTGTAAGTGCTTTTATATTAGTTTACGGAGGGAGT
ATTTAGAAAGCGTAGGGAGTACTTAGTATTTAGATCGGTAAATTCACCTTCGTCTTACCC
TTCCGGCAAAAACAGGTGTTGCTCTCGTAGCGCTCGCTCTCACCCACCCTTCCCCAACTC
GCATCCAGCGCCGCAACCCCTCGTCTCTCCCCCCCTTCCGATCTGAGGCGTCGTTGGAGA
TCGGCGGCAACCGAAGAGGCGTCCGACGACGGCCGTCGCGGGTGGCACCAGTGCAGTGGA
GCAAATCAACCAGTTGAGATGGCGACATTGAGGCCGCTGAGCGTGGAGGAGGTGCTGAGG
GTGAACGGCAGCCACCGCTTTGCCGCCGCGCTGGCTGCCGCCTCCCCCTTTGATTCTCTT
GCCAACGCGCTCCTTGCCGCCCGCCGCATCTGGCTGAACGAGGTGGACGTGACTGGATGG
CTGGAGGCCTTCGCTGCCCACCCACCCATCGGAAGCACCTCCTCCTCCGTCTCCAAGTGG
AGCAAGGAAGAGCAATCAGCTGCTCTTTCCACAGCCACTGATTCGACTGCGCAGGAGTTG
TCCGAGTGGAATGCCAAATACAGGGAGAAGTTTGGGTTCGTGTTCATGATATGCGCATCT
GGGAGGACTGCCCCTGAGGTCTTAGCTGAGCTTAAGAGGCGTTATGCAAATAGACCAGTT
GTTGAGCTTGAGGCTGCGGCAGAGGAAGAACTGAAGATAACTGAGCTGCGTCTTGCAAAG
CTTTTCGCATCAGAAACTGCTGCTCCCCCTACTTCAGGTGAAAATCAGATTAGCCAACCG
GATAAAGCAGCAGGCAACTCCAACCGGACACGCCCTCCTATCACAACCCATGTGCTGGAC
ACGGCTCTTGGATCGCCAGCATCTGGAATTGAAGTTCACCTGGAGATGTGGAAGGACGCG
TCAAGTACCCCGTCATTTGACAACAAAGATTTCAAGGGATGGACAACCCTAGGCTCTTCG
ATTACAAACAATGATGGACGCAGCGGTCAGCTGATGGACATCGTTGACAATGTCACTCCT
GGTTTCTACCGCATAAGTTTCAATACCTCCAAGTATGCACCGTCAGGGTTCTTCCCTTAC
GTGAGCATCATATTTGAGATAAAAAGAAGCCAGGCGACCGAGCATTTCCATGTGCCTCTT
TTACATTCTCCTTTTTCCTTTACCACTTACCGTGGCAGCTAAGCTGTCAATTTGTGTGTA
AATCACATCGAGTGATGGTATTGTTCTGAAACAAGCATAAATGGTCGTAAATCAGGGTGT
TTAGATGTCACTGACATTGTGATATTTGAATAATAATGTTCCATGTAATAATAAGCTCGA
GTATGCAGTGACATTGGATCAGTTTGTTTTCAATACTTTTATCCATTGCTATTTGTGATT
GGGTGGCCTTGAGTGTGGTATTACATCTCTACTTCAGATTTGACATGTCGCATACTTTAG
GCTAGTCATAATGGGGAGTGTCATGTATCTATGTGACATTGGTCCA



Protein Sequence (307 aa)

>BART1_0-u29736.002 307 150831_barley_pseudomolecules
MATLRPLSVEEVLRVNGSHRFAAALAAASPFDSLANALLAARRIWLNEVDVTGWLEAFAA
HPPIGSTSSSVSKWSKEEQSAALSTATDSTAQELSEWNAKYREKFGFVFMICASGRTAPE
VLAELKRRYANRPVVELEAAAEEELKITELRLAKLFASETAAPPTSGENQISQPDKAAGN
SNRTRPPITTHVLDTALGSPASGIEVHLEMWKDASSTPSFDNKDFKGWTTLGSSITNNDG
RSGQLMDIVDNVTPGFYRISFNTSKYAPSGFFPYVSIIFEIKRSQATEHFHVPLLHSPFS
FTTYRGS