Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u29736.003

ChromosomeExonStartStopDirection
chr4H1483706267483705899+
chr4H2483706465483706392+
chr4H3483706600483706543+
chr4H4483706780483706679+
chr4H5483707382483707226+
chr4H6483712153483711486+


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
morexEMB0.00001071920.0001725440.0000447481
morexETI5.064440.00006325330.875725
morexLEA0.000132930.0001642370.000920982
morexEPI0.04501152.4536910.0572
morexROO00.00000111940.0000000203767
morexROO20.02441140.02007312.88685
morexNOD05.07280.00200728
morexRAC4.33852.880780.358281
morexINF10.0000006630180.000008399930.000601552
morexINF20.000005440410.01438720.0217155
morexCAR500.02113150.0879777
morexCAR150.0003086430.00284710.0764261
morexLEM0.4701160.0009343410.00118126
morexLOD0.8203461.327920.0444622
morexPAL0.07378790.3864210.00447084
morexSEN1.692981.363930.418898



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os03g27320.1 +1 9e-151 433 243/286 (85%) protein|steroid binding protein, putative, expressed
TAIR PP10 AT5G58220 @ ARAPORT
AT5G58220.1 @ TAIR		 +1 1e-85 266 155/289 (54%) Symbols: TTL | transthyretin-like protein | chr5:23554546-23555861 REVERSE LENGTH=324
BRACH PP3 Bradi1g60700.1.p +1 5e-160 456 254/285 (89%) pacid=32804008 transcript=Bradi1g60700.1 locus=Bradi1g60700 ID=Bradi1g60700.1.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 (1428 bp)

>BART1_0-u29736.003 1428 150831_barley_pseudomolecules
GTAAATTCACCTTCGTCTTACCCTTCCGGCAAAAACAGGTGTTGCTCTCGTAGCGCTCGC
TCTCACCCACCCTTCCCCAACTCGCATCCAGCGCCGCAACCCCTCGTCTCTCCCCCCCTT
CCGATCTGAGGCGTCGTTGGAGATCGGCGGCAACCGAAGAGGCGTCCGACGACGGCCGTC
GCGGGTGGCACCAGTGCAGTGGAGCAAATCAACCAGTTGAGATGGCGACATTGAGGCCGC
TGAGCGTGGAGGAGGTGCTGAGGGTGAACGGCAGCCACCGCTTTGCCGCCGCGCTGGCTG
CCGCCTCCCCCTTTGATTCTCTTGCCAACGCGCTCCTTGCCGCCCGCCGCATCTGGCTGA
ACGAGGTAGGTGGACGTGACTGGATGGCTGGAGGCCTTCGCTGCCCACCCACCCATCGGA
AGCACCTCCTCCTCCGTCTCCAAGTGGAGCAAGGAAGAGCAATCAGCTGCTCTTTCCACA
GCCACTGATTCGACTGCGCAGGAGTTGTCCGAGTGGAATGCCAAATACAGGGAGAAGTTT
GGGTTCGTGTTCATGATATGCGCATCTGGGAGGACTGCCCCTGAGGTCTTAGCTGAGCTT
AAGAGGCGTTATGCAAATAGACCAGTTGTTGAGCTTGAGGCTGCGGCAGAGGAAGAACTG
AAGATAACTGAGCTGCGTCTTGCAAAGCTTTTCGCATCAGAAACTGCTGCTCCCCCTACT
TCAGGTGAAAATCAGATTAGCCAACCGGATAAAGCAGCAGATCGGATGCGGATTATTGGT
GCACACCTTGGAGCTCTTTCCCAGCTTTCTGCCTATAAAGCTCCTGAAATTACAGGCAAC
TCCAACCGGACACGCCCTCCTATCACAACCCATGTGCTGGACACGGCTCTTGGATCGCCA
GCATCTGGAATTGAAGTTCACCTGGAGATGTGGAAGGACGCGTCAAGTACCCCGTCATTT
GACAACAAAGATTTCAAGGGATGGACAACCCTAGGCTCTTCGATTACAAACAATGATGGA
CGCAGCGGTCAGCTGATGGACATCGTTGACAATGTCACTCCTGGTTTCTACCGCATAAGT
TTCAATACCTCCAAGTATGCACCGTCAGGGTTCTTCCCTTACGTGAGCATCATATTTGAG
ATAAAAAGAAGCCAGGCGACCGAGCATTTCCATGTGCCTCTTTTACATTCTCCTTTTTCC
TTTACCACTTACCGTGGCAGCTAAGCTGTCAATTTGTGTGTAAATCACATCGAGTGATGG
TATTGTTCTGAAACAAGCATAAATGGTCGTAAATCAGGGTGTTTAGATGTCACTGACATT
GTGATATTTGAATAATAATGTTCCATGTAATAATAAGCTCGAGTATGCAGTGACATTGGA
TCAGTTTGTTTTCAATACTTTTATCCATTGCTATTTGTGATTGGGTGG



Protein Sequence (223 aa)

>BART1_0-u29736.003 223 150831_barley_pseudomolecules
MICASGRTAPEVLAELKRRYANRPVVELEAAAEEELKITELRLAKLFASETAAPPTSGEN
QISQPDKAADRMRIIGAHLGALSQLSAYKAPEITGNSNRTRPPITTHVLDTALGSPASGI
EVHLEMWKDASSTPSFDNKDFKGWTTLGSSITNNDGRSGQLMDIVDNVTPGFYRISFNTS
KYAPSGFFPYVSIIFEIKRSQATEHFHVPLLHSPFSFTTYRGS