Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u10054.001

ChromosomeExonStartStopDirection
chr2H1196025359196024513+
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
morexEMB5.7623611.75325.75183
morexETI2.720321.664511.24073
morexLEA0.00001557856.196243.12504
morexEPI2.001720.8356771.42975
morexROO1.748350.008318323.58613
morexROO21.534821.204241.26228
morexNOD1.930550.7051522.81739
morexRAC1.59941.547441.96939
morexINF114.761923.225417.3146
morexINF219.737916.182415.1657
morexCAR54.406784.122024.43228
morexCAR156.01442.136752.42806
morexLEM0.3694450.5793981.2327
morexLOD1.861870.2630830.54158
morexPAL2.658671.717731.24775
morexSEN3.139191.481340.166981



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os07g37610.1 +3 0.0 566 288/390 (74%) protein|B3 DNA binding domain containing protein, putative, expressed
TAIR PP10 AT4G32010 @ ARAPORT
AT4G32010.1 @ TAIR		 +3 3e-72 242 115/152 (76%) Symbols: HSL1, HSI2-L1, VAL2 | HSI2-like 1 | chr4:15481231-15484897 FORWARD LENGTH=780
BRACH PP3 Bradi1g24720.4.p +3 0.0 611 309/400 (77%) pacid=32795972 transcript=Bradi1g24720.4 locus=Bradi1g24720 ID=Bradi1g24720.4.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 (1334 bp)

>BART1_0-u10054.001 1334 150831_barley_pseudomolecules
GTTAGGCACCAAGTCAGATGTGGTCAACTCCTACTGTGCATATGCCTCAAAATGTTGCTG
ACAGAAAGGACAGTTATGTAAAGAGTTGGAGACCTCCTGCGGGCCAGATTTCAAGTCAGT
GGCGACAGAATCACCAGCTGTGGAACATGTCCAGTATACAGACGGACTTGCAGCAACGTC
TAGCTTATGAGTTTGATAGGCCAAGTGGCAGTGAAAAATTACCTCCAGGGCGCACTTTTA
TTCATGCCCAGGAAAAGAAATCCGATGACATGCATGACAGACCAACGACACCTGCCGGCA
TGGGCCAGATTATAAGGGACAGATATGCCAATGGGCTCGGACAGCAAACAAACATGGATC
CGACACACTCCTCTACGCCCTACCAGAGAGAAGGACCAAATCAAAATAGCCTTCATGATC
CTAGTCACCATGTAGGAGAAAGTGACCCTTTGTCTTCAAGGAAAGGGATAGTTTCAGATG
GTGGTTCTACTGCATCTACTGGCTTTAAGCTTGATCCACATCATCCATCCATTCTAAAGG
ATGATGCGGCATCAACCCTGCCGACAATGGGTGGCTACACTATCACTAATTATCCACCGG
TACCTGGACGAAGCGACCATCTCAGAATCATACCTAATAATCCGCAACAACCACCCACCA
CGGTGCCCGTCTCAGTAGTGCAGAAACAGTTCTATTCCCATAGTGTCATTGAGCCCGACT
ACCAAGCGCAATTCCGTAATGGAAAGCCCAGAATGGAGTCCAGAATGGATGCAAAGGCGA
GATCTCAATTACTTCCCCGCTACTGGCCTAGAATAACAGATAAAGAGCTACAGCACTTAT
CGGGAGATTCGAATTCTGTTATTACTCCTTTGTTCGAGAAAATGTTAAGTGCCAGTGATG
CTGGTCGGATTGGTCGTTTGGTGTTGCCAAAGAAATGCGCCGAGGCATACTTCCCCCCAA
TCTCTCAGCCAGAAGGACTTCCCTTAAAAGTTCAGGATGCCAGTGGTAAGGAATGGGTGT
TCCAGTTCCGTTTCTGGCCCAATAATAACAGCAGGATGTATGTATTGGAGGGTGTCACAC
CTTGCATTCAGTCGATGCACTTACAAGCGGGCGATACAGTAAGTTTCAGCCGAATAGATC
CAGAAGGGAAGCTGGTCATGGGATTCAGAAAGACAAAGACTCAAGAACAGGTACATGATG
GTACTTATGTGTGTTGTGTTGTGGCTCCCCTGCAGGAAAGCTCTGTACATTCAGTCTTCT
GTTACAGTTCATTCAGCTTGTATATCACCATTTGCTTGAATGGATGGTCAATGCAGATTC
GACTATGTTCTTCT



Protein Sequence (439 aa)

>BART1_0-u10054.001 439 150831_barley_pseudomolecules
MWSTPTVHMPQNVADRKDSYVKSWRPPAGQISSQWRQNHQLWNMSSIQTDLQQRLAYEFD
RPSGSEKLPPGRTFIHAQEKKSDDMHDRPTTPAGMGQIIRDRYANGLGQQTNMDPTHSST
PYQREGPNQNSLHDPSHHVGESDPLSSRKGIVSDGGSTASTGFKLDPHHPSILKDDAAST
LPTMGGYTITNYPPVPGRSDHLRIIPNNPQQPPTTVPVSVVQKQFYSHSVIEPDYQAQFR
NGKPRMESRMDAKARSQLLPRYWPRITDKELQHLSGDSNSVITPLFEKMLSASDAGRIGR
LVLPKKCAEAYFPPISQPEGLPLKVQDASGKEWVFQFRFWPNNNSRMYVLEGVTPCIQSM
HLQAGDTVSFSRIDPEGKLVMGFRKTKTQEQVHDGTYVCCVVAPLQESSVHSVFCYSSFS
LYITICLNGWSMQIRLCSS