Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u05011.004

ChromosomeExonStartStopDirection
chr1H1500894741500894021-
chr1H2500896865500896331-
chr1H3500897339500896985-


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
morexEMB4.310274.92312.15138
morexETI2.789063.850765.96046
morexLEA2.794011.473771.24721
morexEPI2.047781.607732.03326
morexROO5.270473.732111.16317
morexROO28.47687.816598.32673
morexNOD10.102421.25675.34743
morexRAC36.071439.313637.4767
morexINF14.88397.09716.54964
morexINF213.104913.440210.0901
morexCAR512.6539.6877310.2249
morexCAR151.182620.9780791.01129
morexLEM10.04436.0763312.4409
morexLOD15.474315.72419.1139
morexPAL17.171915.916118.6043
morexSEN1.818591.380951.43558



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os05g37900.1 +1 1e-88 274 159/217 (73%) protein|zinc finger, C3HC4 type domain containing protein, expressed
TAIR PP10 AT5G05830 @ ARAPORT
AT5G05830.1 @ TAIR		 +1 7e-45 157 89/159 (56%) Symbols: | RING/FYVE/PHD zinc finger superfamily protein | chr5:1755910-1756825 FORWARD LENGTH=204
BRACH PP3 Bradi2g23610.2.p +1 3e-94 288 177/240 (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 (1611 bp)

>BART1_0-u05011.004 1611 150831_barley_pseudomolecules
CCTCGCCTCCTCCTGTTCCTCCCCCGACAAGCACAGAACTCGTCTTTTCTCCTTTCTCTT
TTCCCCCTCGCCTCACTCACTCACTGCCAGTACAGTACAATCCCTCCGCTCTTTATTCCC
CTCGCCTCCGACTCGCCCTTGTCCCCTTGCGTGTCCGTCCCGCGGTCATGGATCAAGAAA
CCTCACGAGAACCCCGCCGCTCCAGCCGTATGTCGCCGCATTAGTCGGGGGGAGGGCCCA
GTCCCCGCCGGATCGCTCCTCGCGATCGCATTGCATGCGCGCCTCTTGATCTTGTCTTTA
TCCTGGACACGGATTGGTTTCCGTCGCCGGATTCGGAGCGGCGGCATTCTGGTTGGCCGC
GTCTGAGGAGGAGGAGCGATGGTCGGCGACGGCGCGCGGTCGGCAGTCGCCGCCGGGGTC
CAAGACATCGAGCTCGGCGAGCGGCGCCGCGGTGATGAGTTCCTGGACGACGACGGCGAG
GAGGAGGAGGAGGAGGGCAGCCAGTACTTCACGGACGCGGAGGACCGGTCGTGGCCCTCG
CACTCGCGCCACGAGTCCGCCGCCTTCGAGGACTGCATCTCGCGGTGCTCCTGCGGCGGC
GCCGACAGCGACGCGGACATCGAGGCCGGCGGCGGGCACTTCAGGAAGTCGTCCTGCGTG
TCCGAGTGCTCGCTGGACGACGTCGACCTGGAGGCCGGGCTGGCCGAGAGCGCCAAGGGC
AGCCCCGACCCCGAGAAGGCCGAGAGGAACTGCCGCATTTGCCACCTCGGCCTCGAGAGC
GCGGCGGCCGAGTCCGGCGCCGGCATCACGCTCGGCTGCTCCTGCAAGGGCGACCTCTCC
TACTCCCACAAGCAGTGCGCCGAGACCTGGTTCAAGATCAGAGGCAACAAGACCTGTGAA
ATTTGCAGCTCAGTCGCATGCAATGTGGTAGTTTTAGGCGATCCAGAGTTCACCGAGCAG
TCGAATGAATCAACTACCGCAGCAGCCGGGCATACATTTCCAACCGAAACTAGGAGGTTT
TGGCAAGGGCACCGGTTCCTCAACTTCCTTCTAGCATGCATGGTTTTCGCCTTCGTCATC
TCATGGCTCTTCCACTTCAATGTCCCGGGGTGAGTTCTCGCAGCCAATGGCCCCTCAATA
AAAGCCACAGGGCCATTGAGGCAAACATGTGGGTCAGATTCAGCAAATCTGGAGAGCGGG
ATGAGGTGAAGTTATTAAGCAGTGAAGAGGTACAAATGAGTGTGTATGTGGGGCGCGACG
GCCTTAAGTTTCTCTGGATCAGGATCCGGTACGAAAGAAGCCCTGATGAAGATCTGCCGC
CGTTCATGAATTTGGGTGAAGGTAGCAAACAGCGAAGAAGAGAAGGTGTGTTGTTCCGGG
ATTGTTTTAGGTTTGAAGGACATGTTTTATGTTAGTGTCGTCGTTTCCTTTAGCTTGGCC
GTTTTCGCCTTGTGAGTTGGTGTGATATGTGCAGATTTTGTTTTATGCCTTCCATCCAGT
GTTTATAATCCTGATAAACAGGATGAGGTGGTAGCTGTGCTTAGCAGGAAGAGAAACCCC
ACTGCCAGCTCAGGTTCCGAATAATGAAGAGAAAATGTTTTTGAGACGCTT



Protein Sequence (244 aa)

>BART1_0-u05011.004 244 150831_barley_pseudomolecules
MVGDGARSAVAAGVQDIELGERRRGDEFLDDDGEEEEEEGSQYFTDAEDRSWPSHSRHES
AAFEDCISRCSCGGADSDADIEAGGGHFRKSSCVSECSLDDVDLEAGLAESAKGSPDPEK
AERNCRICHLGLESAAAESGAGITLGCSCKGDLSYSHKQCAETWFKIRGNKTCEICSSVA
CNVVVLGDPEFTEQSNESTTAAAGHTFPTETRRFWQGHRFLNFLLACMVFAFVISWLFHF
NVPG