Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u10054.002

ChromosomeExonStartStopDirection
chr2H1196025377196024513+
chr2H2196025614196025518+
chr2H3196026644196026470+
chr2H4196028005196027791+


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
morexEMB0.9708750.1353742.05432
morexETI0.6461720.3347060.00186173
morexLEA6.258870.7075050.213705
morexEPI0.002795741.687030.0584779
morexROO0.1319731.439810.552298
morexROO20.5082370.5042820.101878
morexNOD1.370150.00007890650.0435155
morexRAC0.803681.452810.247859
morexINF15.677680.9581971.93304
morexINF21.512560.003199660.0000000468122
morexCAR52.50846.880896.1614
morexCAR150.6658281.256283.06173
morexLEM0.2436831.082190.222237
morexLOD0.4094321.511780.881614
morexPAL0.2128790.07442370.106497
morexSEN0.003901240.06846370.793207



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os07g37610.1 +3 0.0 559 287/396 (72%) protein|B3 DNA binding domain containing protein, putative, expressed
TAIR PP10 AT4G32010 @ ARAPORT
AT4G32010.1 @ TAIR		 +3 1e-74 248 117/154 (76%) Symbols: HSL1, HSI2-L1, VAL2 | HSI2-like 1 | chr4:15481231-15484897 FORWARD LENGTH=780
BRACH PP3 Bradi1g24720.3.p +3 0.0 618 312/406 (77%) pacid=32795971 transcript=Bradi1g24720.3 locus=Bradi1g24720 ID=Bradi1g24720.3.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 (1352 bp)

>BART1_0-u10054.002 1352 150831_barley_pseudomolecules
GTTAGGCACCAAGTCAGATGTGGTCAACTCCTACTGTGCATATGCCTCAAAATGTTGCTG
ACAGAAAGGACAGTTATGTAAAGAGTTGGAGACCTCCTGCGGGCCAGATTTCAAGTCAGT
GGCGACAGAATCACCAGCTGTGGAACATGTCCAGTATACAGACGGACTTGCAGCAACGTC
TAGCTTATGAGTTTGATAGGCCAAGTGGCAGTGAAAAATTACCTCCAGGGCGCACTTTTA
TTCATGCCCAGGAAAAGAAATCCGATGACATGCATGACAGACCAACGACACCTGCCGGCA
TGGGCCAGATTATAAGGGACAGATATGCCAATGGGCTCGGACAGCAAACAAACATGGATC
CGACACACTCCTCTACGCCCTACCAGAGAGAAGGACCAAATCAAAATAGCCTTCATGATC
CTAGTCACCATGTAGGAGAAAGTGACCCTTTGTCTTCAAGGAAAGGGATAGTTTCAGATG
GTGGTTCTACTGCATCTACTGGCTTTAAGCTTGATCCACATCATCCATCCATTCTAAAGG
ATGATGCGGCATCAACCCTGCCGACAATGGGTGGCTACACTATCACTAATTATCCACCGG
TACCTGGACGAAGCGACCATCTCAGAATCATACCTAATAATCCGCAACAACCACCCACCA
CGGTGCCCGTCTCAGTAGTGCAGAAACAGTTCTATTCCCATAGTGTCATTGAGCCCGACT
ACCAAGCGCAATTCCGTAATGGAAAGCCCAGAATGGAGTCCAGAATGGATGCAAAGGCGA
GATCTCAATTACTTCCCCGCTACTGGCCTAGAATAACAGATAAAGAGCTACAGCACTTAT
CGGGAGAGTATCCAAAAAACTCTACTTCGAATTCTGTTATTACTCCTTTGTTCGAGAAAA
TGTTAAGTGCCAGTGATGCTGGTCGGATTGGTCGTTTGGTGTTGCCAAAGAAATGCGCCG
AGGCATACTTCCCCCCAATCTCTCAGCCAGAAGGACTTCCCTTAAAAGTTCAGGATGCCA
GTGGTAAGGAATGGGTGTTCCAGTTCCGTTTCTGGCCCAATAATAACAGCAGGATGTATG
TATTGGAGGGTGTCACACCTTGCATTCAGTCGATGCACTTACAAGCGGGCGATACAGTAA
GTTTCAGCCGAATAGATCCAGAAGGGAAGCTGGTCATGGGATTCAGAAAGACAAAGACTC
AAGAACAGGTACATGATGGTACTTATGTGTGTTGTGTTGTGGCTCCCCTGCAGGAAAGCT
CTGTACATTCAGTCTTCTGTTACAGTTCATTCAGCTTGTATATCACCATTTGCTTGAATG
GATGGTCAATGCAGATTCGACTATGTTCTTCT



Protein Sequence (445 aa)

>BART1_0-u10054.002 445 150831_barley_pseudomolecules
MWSTPTVHMPQNVADRKDSYVKSWRPPAGQISSQWRQNHQLWNMSSIQTDLQQRLAYEFD
RPSGSEKLPPGRTFIHAQEKKSDDMHDRPTTPAGMGQIIRDRYANGLGQQTNMDPTHSST
PYQREGPNQNSLHDPSHHVGESDPLSSRKGIVSDGGSTASTGFKLDPHHPSILKDDAAST
LPTMGGYTITNYPPVPGRSDHLRIIPNNPQQPPTTVPVSVVQKQFYSHSVIEPDYQAQFR
NGKPRMESRMDAKARSQLLPRYWPRITDKELQHLSGEYPKNSTSNSVITPLFEKMLSASD
AGRIGRLVLPKKCAEAYFPPISQPEGLPLKVQDASGKEWVFQFRFWPNNNSRMYVLEGVT
PCIQSMHLQAGDTVSFSRIDPEGKLVMGFRKTKTQEQVHDGTYVCCVVAPLQESSVHSVF
CYSSFSLYITICLNGWSMQIRLCSS