Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u18690.015

ChromosomeExonStartStopDirection
chr3H16742539867425185-
chr3H26742568067425530-
chr3H36742598467425751-
chr3H46742625967426201-
chr3H56742695067426694-
chr3H66742718967427047-
chr3H76742733267427278-
chr3H86742750667427429-
chr3H96742771767427601-
chr3H106742848667427863-


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
morexEMB0.099855400
morexETI000
morexLEA000
morexEPI000
morexROO000
morexROO20.15064300
morexNOD000
morexRAC000
morexINF1000
morexINF2000
morexCAR5000
morexCAR15000
morexLEM0.14703400
morexLOD000
morexPAL000
morexSEN000.116702



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os01g08700.6 +1 0.0 424 199/233 (85%) protein|GIGANTEA, putative, expressed
TAIR PP10 AT1G22770 @ ARAPORT
AT1G22770.1 @ TAIR		 +1 7e-95 317 155/246 (63%) Symbols: GI, FB | gigantea protein (GI) | chr1:8062398-8067447 FORWARD LENGTH=1173
BRACH PP3 Bradi2g05226.1.p +1 0.0 454 212/227 (93%) pacid=32776210 transcript=Bradi2g05226.1 locus=Bradi2g05226 ID=Bradi2g05226.1.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 (1932 bp)

>BART1_0-u18690.015 1932 150831_barley_pseudomolecules
GTGCCATTTACGTCCAAGGCAGCCATCTCTCCAACTCGAGGAATCATGTTGAGCAGAATT
GGGTCTGGGACCAATGATGAAGATGAGTAGATGACTGAGCCCTTGGATCCTGATCCAAGG
GTCAGAGTTGGCGATTAGATGTGTTCCTATACTATCTTATTTCCCCAAGCATCTGGAATC
ATTCCATTCCATCCCATTCTCAAATCTCAAAGTCCAGGATGGTTCCATTCCAGTCTACTT
CATTCCTCAAACCACTAACGGTTTTAGAGTTGAAATCCTTTTTCTGACTCTGTTAAGGGC
TGGGAATGTAAACGAGACTTCTTTTTAGAAATATGTTGCCAAGGCTATGCAAAATTTGTT
CCATTGGCTGGTTGACCTCCTCTCTTGTCAATTTATGGCAATATTTCTTGTTTTAAAATT
TATTAAAATGACATCTATAATAATGTCCCTTTCCTTCTTTCGACTTTCCTTTTGCTATAT
TTTGCAATGCAGAGACGTTAAGCGCCTATGGTTGGAACTGGTTGATATGATATCTGGTCA
CATTGTGGGATGCAATCCCCCCTTAGTGGGGGGTGATTGAAGAAGTCAACAATAGGAGAA
CTTGCATCTTGCTGAAGTTTTCTGTTTCTTGAGCAGGCTCTTAAACTACCAAGTATGTCA
GCGTCAAATGGGAAGTGGATTGATGGACTCCAGTTCTCATCACTGTTCTGGCCCCCGCCA
CACGATGCGCAGCAGAAACAGGCACAAATTTTAGCCTATGTTGAGTACTTTGGTCAGTTC
ACATCTGACAGCGAGCAATTCCCGGAGGATGTAGCTCAGCTAATTCAAACTTGCTATCCA
TCAAAAGAAAAGCGGTTGGTAGATGAAGTATTAGCAACTTTTGTTCTCCATCACCCCGAG
CATGGTCATGCAGTTGTACATCCAATTCTTTCACGCATCATAGACGGGACACTGAGTTAT
GATAGTCATGGTTCCCCATTCAATTCCTTCATCTCCTTATTTACCCAAAGTTCTGAGAAA
GAGTACTCAGAGCAGTGGGCCTTGGCCTGTGGAGAGATTCTTAGAGTTCTAACTCACTAC
AACAGGCCAATCTTTAAAGTTGCAGACTGTAACAACACCTCTGACCAGGCTACAACAAGT
TGTTCTGCACAGGAGAAAGCTAATTACTCTCCAGGAAATGAACCTGAACGGAAGCCATTG
AGGCCATTATCTCCTTGGATCACAGATATTTTGCTAACTGCACCTTTAGGCATTAGAAGC
GACTATTTTAGATGGTGTGGTGGAGTTATGGGAAAATACGCAGCTGGTGGAGAATTGAAG
CCTCCAACAACTGCCGAGGAGCTGGTAAGCACCCACAACTCATGCCATCCACCCCAAGAT
GGGCTGTTGCCAATGGAGCTGGAGTTATTTTAAGTGTCTGTGATGAGGAAGTAGCTCGTT
ATGAGACAGCAAACTTAACCGCGGCAGCTGTTCCCGCCCTTCTGCTACCTCCACCGACAA
CACCCTTGGATGAGCATTTGGTGGCAGGGCTACCCCCTCTTGAGCCATACGCTCGCTTGT
TTCATAGATACTATGCAATTGCCACACCAAGTGCTACACAAAGATTGCTTTTTGGTCTTC
TTGAAGCACCACCATCATGGGCTCCAGATGCACTTGATGCAGCAGTTCAGCTTGTTGAAC
TCCTTCGGGCAGCTGAAGATTATGCTACTGGCATGCGGCTTCCAAAAAATTGGTTGCATC
TTCATTTCTTGCGTGCGATTGGAACTGCAATGTCTATGAGGGCTGGTATTGCTGCCGATA
CAGCTGCTGCGTTGCTTTTTCGCATACTATCCCAACCAACGTTGCTTTTTCCTCCACTAA
GGCATGCTGAAGGAGTTGAAGTGCAACATGAACCACTGGGTGGCTATGTATCATCATACA
AAAGACAGGTAT



Protein Sequence (220 aa)

>BART1_0-u18690.015 220 150831_barley_pseudomolecules
MVWWSYGKIRSWWRIEASNNCRGAGKHPQLMPSTPRWAVANGAGVILSVCDEEVARYETA
NLTAAAVPALLLPPPTTPLDEHLVAGLPPLEPYARLFHRYYAIATPSATQRLLFGLLEAP
PSWAPDALDAAVQLVELLRAAEDYATGMRLPKNWLHLHFLRAIGTAMSMRAGIAADTAAA
LLFRILSQPTLLFPPLRHAEGVEVQHEPLGGYVSSYKRQV