Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u20608.002

ChromosomeExonStartStopDirection
chr3H1358149252358148864+
chr3H2358149679358149564+
chr3H3358149891358149809+
chr3H4358150386358150265+
chr3H5358152519358152355+
chr3H6358152688358152595+
chr3H7358153398358153224+
chr3H8358154295358153493+


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
morexEMB17.913124.597432.1682
morexETI18.453212.308714.9778
morexLEA14.531315.359525.0216
morexEPI9.392913.27648.44611
morexROO11.681111.25365.34925
morexROO218.864320.383920.0502
morexNOD12.853510.601415.9947
morexRAC13.99614.874916.183
morexINF127.808224.237822.2646
morexINF28.7593411.947314.8473
morexCAR522.195418.558320.3523
morexCAR152.399632.652294.49811
morexLEM15.314312.925515.2243
morexLOD10.413216.641210.0853
morexPAL11.154812.016112.038
morexSEN26.474920.431320.7852



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os01g39790.1 +2 1e-139 409 203/273 (74%) protein|esterase/lipase/thioesterase, putative, expressed
TAIR PP10 AT1G29840 @ ARAPORT
AT1G29840.1 @ TAIR		 +2 5e-97 298 143/247 (58%) Symbols: | alpha/beta-Hydrolases superfamily protein | chr1:10445735-10447422 REVERSE LENGTH=263
BRACH PP3 Bradi2g41780.1.p +2 9e-159 457 222/267 (83%) pacid=32782108 transcript=Bradi2g41780.1 locus=Bradi2g41780 ID=Bradi2g41780.1.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 (1947 bp)

>BART1_0-u20608.002 1947 150831_barley_pseudomolecules
ATACGGCTTCTGTTCAAACACGCTAGTTTTCGATCCGCAAACGCGATCTTTGTAAAACCG
CAAACGCGTTTTGCGGGTAAGTTTGGGCCAACCCACGAGAGCGCGAGCAAGAAATCCTAA
TCCAACGGCTTCCAGCCCTTCGCGTTATCATTGGGTCCATCCAATGTAGCGCCTTCCTAG
TGCGTTCTTTTCTTTGTACACCTTAAATTCCACGCCCTCCTCTGGCGTCCTCCACTTGCC
CGGCGAATCTAACCTTCATCCTGCTGCTGCCACCGCCGGCGGGTCGACTAGACTCGGGTT
CCTCCCACCCCAAACAGCACGAGGCTGCCGCCGCCATCTGTCTTCCATGTCACAGCCGCT
CAATTCCTCCCGGCATGCTTCCAATCCCCATGCTACACAGAGGGTATTGATAACGAACAA
GCGTGGAGAGAAACTTGTGGGGCTACTGCATCCCACGGGTTTGAACAAGATTGTAGTCTT
GTGCCATGGCTTTACGGCCTCCAAGAGTTCTGGCATTATTGTTGATCTGGCAGATGCAAT
AATAAAAAAAGGGATTAGTGTCTTTCACTTTGATTTCAGTGGAAACGGAGAGAGCGAAGG
CGAATTCCAGTATGGCAACTACAGGAAAGAGGCTGAAGACTTGCATTCTGTTGTCTCATA
TCTGTATCAGGAGAAGTATGATGTAGCAGCTGTTGTTGGTCACAGCAAAGGAGGAGATGT
GGTTGTTCTTTATGCTTCCCTATATGACGATGTCCACATGGTTGTTAACCTATCTGGCCG
ATTTTATTTGGAGAAAGGCATTGAGGAACGCCTAGGGAAGGAATTTCTTGACAGAATAAA
TAAGGAAGGTTACATTGATGTCACAAACAAGTCAGGAAATATGTTATACAGGGTAACAAA
AGAGAGCTTGATGGAACGACTCAACACTGACATGCGTGCAACGAGCCTCTCCATTAGCAA
GGAATGCAGCTTCTTCACAGTTCATGGTTCTGCTGATGACATCATTCCGGTGGAAGATGC
ATATGAGTTTGCAAAGCATATACCAACCCACAAACTCTGTGTCGTCGAGGGAGCAGATCA
CTGCTACACCAGACATCGTAAAGAACTTTCAGATGCTGTAGTGGGTTTCATTACATCCAA
CAAGGCCAGGGATACCACGCTAGAAGATCAATGAATTCTGATGGATTTATGCTGTAGGAT
TTTGTACAGCAGTTCTCTTTACAGAAGCTCCCCTCAGAACAAGGCAATTCTAGATCATGG
TCATTCTACTTCTTAGTTCCGGGATGTAATAAGCAATAAAGCATTGCAAGGCTTTAGGTT
TGCGTTATTTTATGGGGACTGCTATGCGTCGGTCCCTTCCAGTGGGATGCACATTTTTCT
ATTTTGCAACAAAGACCTTGTTGCAGAAACATTTATAACGGAGATTGTGTTGGAGAATTT
TTATGTAACAGAGGTTGTGTTGCGATTTTTTTTTGCAAGAGAGACCGTGTTATAATTTTT
TTGCAACATGAGTGTTGTTTTGGAAAAAAACACAAACGATGTTGCAGAAAATATTTGCAG
TTTTTTTTTGKCAACGTAGGTGTTGTTGCGAAGAGCAAATTTGCAACACACGTGATGTTG
GAGGAAGAGAGGTGCAAAGGTACGTGTGTACACGCATTGCACAGATGAGATGGCGGATTG
CTCGCGTGCGATCTGCCGGCTGAAGTTAAGTATTTTCCTTATTTTATTAGCTAAATAGTT
GGAAAAGTATGCTGTAAAATATGTGAAACTATTATAGAGGTGTTTTGGAGCTCGGGGTGC
GTGGACTCTGAAATTTTCATTTAGAAAAACTCACATCCAAAGTGTAATAATTTCTGAAAA
CAATTACATGTGCATATGAATGTACTGATATGAGATAACATGTGAGCTATACAAATAAAA
GACAAAATCATGGATTTTTAATAGCAA



Protein Sequence (275 aa)

>BART1_0-u20608.002 275 150831_barley_pseudomolecules
MSQPLNSSRHASNPHATQRVLITNKRGEKLVGLLHPTGLNKIVVLCHGFTASKSSGIIVD
LADAIIKKGISVFHFDFSGNGESEGEFQYGNYRKEAEDLHSVVSYLYQEKYDVAAVVGHS
KGGDVVVLYASLYDDVHMVVNLSGRFYLEKGIEERLGKEFLDRINKEGYIDVTNKSGNML
YRVTKESLMERLNTDMRATSLSISKECSFFTVHGSADDIIPVEDAYEFAKHIPTHKLCVV
EGADHCYTRHRKELSDAVVGFITSNKARDTTLEDQ