Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u05042.012

ChromosomeExonStartStopDirection
chr1H1501617123501616727-
chr1H2501617377501617276-
chr1H3501618080501617967-
chr1H4501618560501618447-
chr1H5501619133501618955-
chr1H6501619663501619229-


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
morexEMB0.550260.0001001771.70278
morexETI31.961331.708230.6546
morexLEA4.97051.472043.7105
morexEPI8.673374.2106110.1983
morexROO2.6076600
morexROO20.8219773.970362.59152
morexNOD015.72928.73928
morexRAC19.280324.495325.167
morexINF101.679142.6856
morexINF21.819673.595963.23001
morexCAR54.907060.09249541.37957
morexCAR150.15233600.331726
morexLEM19.488616.086820.0452
morexLOD18.049412.818520.7574
morexPAL24.602920.72121.5969
morexSEN10.79586.327937.82964



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os08g06280.7 +2 8e-44 111 74/74 (100%) protein|LSD1 zinc finger domain containing protein, expressed
TAIR PP10 AT1G32540 @ ARAPORT
AT1G32540.1 @ TAIR		 +2 1e-38 108 69/75 (92%) Symbols: LOL1 | lsd one like 1 | chr1:11768253-11769591 FORWARD LENGTH=187
BRACH PP3 Bradi3g16400.3.p +2 5e-44 111 74/74 (100%) pacid=32812785 transcript=Bradi3g16400.3 locus=Bradi3g16400 ID=Bradi3g16400.3.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 (1341 bp)

>BART1_0-u05042.012 1341 150831_barley_pseudomolecules
GCGTAGTGAGTTTCGACGGGGCCCACATGGCATAGGGGATAAGAAAGAGAATCCACGTTC
CCAGCCACAGTGCCGTGCTTTACCTTATCTGCCGCATTCCAACTCATGTTGTTATTCTGA
GCAAAACTCGACTCGCTCGCTCGTCTCGACATCTGCACCGGATCGAGCTCAGCAAAGCCC
GAGCCGGAGGCGCTCGTCTGCCCGGGGAGCGGCGCCATGCGGGTCCGCCTCTTCCTCTGA
ACCGGGCAAGCGCGAGCCGCCTTCTTCCTCCGGCTCGGCGTCGGCGGCGACGACGAGCGT
CGGTGGCGGCATAGCACGGTCCAGCGACGAGCAGGTGATTCGGCGCCCAGCTCTGCTGCC
GCGACGAGCGCTGAAGGCGGCTCTCCGTCTGTCTAATTTGACGCTCGATTTGCCTCAGGC
CTGCACGGCTCAACTGATTTCATGTAGAGGAGGGCAATCTGTTCTCATCCCCTCGACTTC
CAGCAGAGCGTGCGAAGTCTCGTCCGCAGCAACGACGACGCCGGCTCAGGCAGCCGCGGG
CACGGCAATGCCGGTTCCTCTTGCCCCTTACCCAACTCCTCCTGCGCCCTTCACGCCACC
CGCTCCCAATGCAGGGGCTCAAAGCCAACTTGTCTGCTCTGGGTGCCGGAATCTGCTCAT
GTATCCTGCCGGCGCAACGTCGGTATGCTGCGCGGTTTGCAGTACCGTGACCGCTGTTCC
GGCTCCTGGGACCGAGATGGCGCAGCTAGTTTGCGGAGGATGCCACACTCTTCTGATGTA
CATACGTGGTGCCACAAGTGTACAGTGTTCTTGCTGCCACACTGTCAACCTGGCAATGGA
AGGTTGCGCATGTAAACTGTGGGAGTTGCCGAATGCTGCTCATGTACCAGTACGGCGCAA
GGTCCGTCAAATGTGCAGTCTGCAGTTTCGTGACATCAGTTGGGGCATCATCGGGTGCAG
AGCAGAAGCCCAGCAACTGAAATCCTGCAAGTTCATTACGAAGGCAGCTTCCCGAAATAA
GAATGCTTTGAGTGCACATGTATAGAGTTCTTCCCAGAAGCAACCTTTTCCTCCCCTCTC
CATTTCTCCCTTCGTTGGACCTGGCGAGCTTGCGGAATAAACAAGAGTTTTTGGTAATAC
ATAGTTGCTCAAAATTCGTCGAATCATCTGTGTAACTGGGTCAGACAGATACATGAACCC
ACCATGTTTATGTTCAAATTTAGCTTCTTTTACTTGTGTTCTATATATTTCAGATTTTTT
TTCTTGTGGTCATCGGAAGAATTTCTTCAGATGTGCTTTGCCGTGCGTATTCTTGAACCG
ATCTATATCACTGCAGACATG



Protein Sequence (347 aa)

>BART1_0-u05042.012 347 150831_barley_pseudomolecules
RSEFRRGPHGIGDKKENPRSQPQCRALPYLPHSNSCCYSEQNSTRSLVSTSAPDRAQQSP
SRRRSSARGAAPCGSASSSEPGKREPPSSSGSASAATTSVGGGIARSSDEQVIRRPALLP
RRALKAALRLSNLTLDLPQACTAQLISCRGGQSVLIPSTSSRACEVSSAATTTPAQAAAG
TAMPVPLAPYPTPPAPFTPPAPNAGAQSQLVCSGCRNLLMYPAGATSVCCAVCSTVTAVP
APGTEMAQLVCGGCHTLLMYIRGATSVQCSCCHTVNLAMEGCACKLWELPNAAHVPVRRK
VRQMCSLQFRDISWGIIGCRAEAQQLKSCKFITKAASRNKNALSAHV