Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u05013.003

ChromosomeExonStartStopDirection
chr1H1500969286500968482-
chr1H2500971410500970876-
chr1H3500971956500971534-


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
morexEMB0.00000759820.000002361372.72315
morexETI000
morexLEA000
morexEPI00.2046430
morexROO0.030512700
morexROO20.4742040.5909620
morexNOD0.1967210.6133570
morexRAC0.47700702.10898
morexINF10.5887380.4837180
morexINF21.109490.4655911.38396
morexCAR500.5550951.27864
morexCAR15000
morexLEM0.2521420.4875870.222181
morexLOD00.02322770.56065
morexPAL1.0675600.241379
morexSEN00.5445760



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os05g37900.1 +3 2e-88 275 159/217 (73%) protein|zinc finger, C3HC4 type domain containing protein, expressed
TAIR PP10 AT5G05830 @ ARAPORT
AT5G05830.1 @ TAIR		 +3 7e-45 158 89/159 (56%) Symbols: | RING/FYVE/PHD zinc finger superfamily protein | chr5:1755910-1756825 FORWARD LENGTH=204
BRACH PP3 Bradi2g23610.2.p +3 5e-94 289 177/240 (74%) pacid=32776793 transcript=Bradi2g23610.2 locus=Bradi2g23610 ID=Bradi2g23610.2.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 (1763 bp)

>BART1_0-u05013.003 1763 150831_barley_pseudomolecules
CATCAGCATCACCCCCGCCCCCATGGCCATAAGACGACGGTGAGCTGATAGCGCCAGACG
GACCAAACCCCTCCTCGCCTCCTCCTGTTCCTCCCCCGACAAGCACAGAACTCGTCTTTT
CTCCTTTCTCTTTTCCCCCTCGCCTCACTCACTCACTGCCAGTACAGTACAATCCCTCCG
CTCTTTATTCCCCTCGCCTCCGACTCGCCCTTGTCCCCTTGCGTGTCCGTCCCGCGGTCA
TGGATCAAGAAACCTCACGAGAACCCCGCCGCTCCAGCCGTATGTCGCCGCATTAGTCGG
GGGGAGGGCCCAGTCCCCGCCGGATCGCTCCTCGCGATCGCATTGCATGCGCGCCTCTTG
ATCTTGTCTTTATCCTGGACACGGATTGGTTTCCGTCGCCGGATTCGGAGCGGCGGCATT
CTGGCCGCGTCTGAGGAGGAGGAGCGATGGTCGGCGACGGCGCGCGGTCGGCAGTCGCCG
CCGGGGTCCAAGACATCGAGCTCGGCGAGCGGCGCCGCGGTGATGAGTTCCTGGACGACG
ACGGCGAGGAGGAGGAGGAGGAGGGCAGCCAGTACTTCACGGACGCGGAGGACCGGTCGT
GGCCCTCGCACTCGCGCCACGAGTCCGCCGCCTTCGAGGACTGCATCTCGCGGTGCTCCT
GCGGCGGCGCCGACAGCGACGCGGACATCGAGGCCGGCGGCGGGCACTTCAGGAAGTCGT
CCTGCGTGTCCGAGTGCTCGCTGGACGACGTCGACCTGGAGGCCGGGCTGGCCGAGAGCG
CCAAGGGCAGCCCCGACCCCGAGAAGGCCGAGAGGAACTGCCGCATTTGCCACCTCGGCC
TCGAGAGCGCGGCGGCCGAGTCCGGCGCCGGCATCACGCTCGGCTGCTCCTGCAAGGGCG
ACCTCTCCTACTCCCACAAGCAGTGCGCCGAGACCTGGTTCAAGATCAGAGGCAACAAGA
CCTGTGAAATTTGCAGCTCAGTCGCATGCAATGTGGTAGTTTTAGGCGATCCAGAGTTCA
CCGAGCAGTCGAATGAATCAACTACCGCAGCAGCCGGGCATACATTTCCAACCGAAACTA
GGAGGTTTTGGCAAGGGCACCGGTTCCTCAACTTCCTTCTAGCATGCATGGTTTTCGCCT
TCGTCATCTCATGGCTCTTCCACTTCAATGTCCCGGGGTGAGTTCTCGCAGCCAATGGCC
CCTCAATAAAAGCCACAGGGCCATTGAGGCAAACATGTGGGTCAGATTCAGCAAATCTGG
AGAGCGGGATGAGGTGAAGTTATTAAGCAGTGAAGAGGTACAAATGAGTGTGTATGTGGG
GCGCGACGGCCTTAAGTTTCTCTGGATCAGGATCCGGTACGAAAGAAGCCCTGATGAAGA
TCTGCCGCCGTTCATGAATTTGGGTGAAGGTAGCAAACAGCGAAGAAGAGAAGGTGTGTT
GTTCCGGGATTGTTTTAGGTTTGAAGGACATGTTTTATGTTAGTGTCGTCGTTTCCTTTA
GCTTGGCCGTTTTCGCCTTGTGAGTTGGTGTGATATGTGCAGATTTTGTTTTATGCCTTC
CATCCAGTGTTTATAATCCTGATAAACAGGATGAGGTGGTAGCTGTGCTTAGCAGGAAGA
GAAACCCCACTGCCAGCTCAGGTTCCGAATAATGAAGAGAAAATGTTTTTGAGACGCTTG
AGCTCTTGTGTCTGCACATGGAAACGTTGCTGGGGAAACTTGTGTTTGTTTCTTCAACGC
TTGTGCTATATGTTTGGCTGCTG



Protein Sequence (244 aa)

>BART1_0-u05013.003 244 150831_barley_pseudomolecules
MVGDGARSAVAAGVQDIELGERRRGDEFLDDDGEEEEEEGSQYFTDAEDRSWPSHSRHES
AAFEDCISRCSCGGADSDADIEAGGGHFRKSSCVSECSLDDVDLEAGLAESAKGSPDPEK
AERNCRICHLGLESAAAESGAGITLGCSCKGDLSYSHKQCAETWFKIRGNKTCEICSSVA
CNVVVLGDPEFTEQSNESTTAAAGHTFPTETRRFWQGHRFLNFLLACMVFAFVISWLFHF
NVPG