Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u42531.007

ChromosomeExonStartStopDirection
chr6H12223703522236800+
chr6H22223782522237685+
chr6H32223897422238862+
chr6H42223929222239057+
chr6H52223974922239402+
chr6H62224036022239832+


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
morexEMB19.860517.63415.0432
morexETI8.8920511.473615.3639
morexLEA7.692930.299782.65956
morexEPI1.528395.078872.16479
morexROO9.2829412.82036.55959
morexROO230.755333.67329.558
morexNOD3.1205312.41357.9404
morexRAC17.750623.181126.4209
morexINF134.477361.907246.6125
morexINF249.976853.801143.0535
morexCAR516.000522.450222.5684
morexCAR1513.707311.325710.6857
morexLEM16.13269.6737510.1515
morexLOD24.159325.95117.4409
morexPAL8.187959.8212612.1914
morexSEN1.423213.814944.31695



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os02g03040.1 +2 1e-126 372 220/261 (84%) protein|RNA recognition motif containing protein, expressed
TAIR PP10 AT5G52040 @ ARAPORT
AT5G52040.1 @ TAIR		 +2 4e-88 275 169/289 (58%) Symbols: ATRSP41, RS41, At-RS41 | RNA-binding (RRM/RBD/RNP motifs) family protein | chr5:21131081-21133318 FORWARD LENGTH=356
BRACH PP3 Bradi3g02226.1.p +2 2e-140 407 241/258 (93%) pacid=32814082 transcript=Bradi3g02226.1 locus=Bradi3g02226 ID=Bradi3g02226.1.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 (1603 bp)

>BART1_0-u42531.007 1603 150831_barley_pseudomolecules
CTCGGCTGCAGGGAGCTCAGATCTGGCGATTTTTTCATATTTTTTTCTTCAATAGGACTC
TAGCTCGCCTTTTGCTCTGCGTCGCTCCGTCTGAGCGGGCGCGCTGGCGGGTTCTGGGCA
TGCACGGGAGAGTTAGGTTCAGCTGCGCCGGACGTGGAAATCTGGCAACGGGGCCTGCCA
CCGAGAGAATCCGTGTGCTGTTTAAGCTGTGATGAAAATTCGCTCGTGGTTGTCAGGTTT
GGGGAAGATCTGTTTATACAGCAACACCAACATGAGGCCAATTTTCTGCGGGAACCTTGA
CTATGATGCCCGCCAATCTGAAGTCGAGCGTCTTTTTGGCAAATATGGAAGAGTGGAGCG
AGTTGACATGAAGACAGGATTTGCGTTCGTCTACATGGAAGATGAACGTGATGCTGAAGA
TGCTATCCGTAGACTTGATAGAACTGACTTTGGTAGAACAGGGAGGAGACTGAGAGTCGA
ATGGACAAAGGAGGATCGCAGTGGTGGTCGGAAAGGAAATGGAAAGAGATCTCCAAGCAG
CGTGAAACCAACCAAAACCTTGTTTGTGATCAACTTTGATCCAATCAACACAAGGACAAG
AGATCTGGAGAAGCACTTTGATCTGTATGGCAAGATTGCAAATATCAGAATCAGAAGGAA
CTTTGCATTTGTCCAGTATGAAACACAGGAGGATGCTACTAAAGCTCTGGACGGTACTAA
TGGAAGCACTGTGATGGACAGGGTGATTTCTGTTGAGTATGCGCTTCGTGACGATGATGA
AAAAAGGAACGGGTACAGTCCAGACAGGAGAGGAGGCCGTGATAGGTCTCCTGACAGAAG
GGACAATCGTGGTAGGTCGGCAAGTCCTTATGGCAGAGGGCGGGAAAGGGGCAGCCCAGA
CTATGGCAGGGGCAGGGAGAGGGGCAGCCCGGACTATGGCAAGGGCGGTGCCAGAGATAG
TCCTGACTATGTCCGTGGTGGAAGCCCGTACGGCGGCAAAGGGGATGACAGGGCTAGCCC
CAAGTATGACCGTGAACGCCGTGAAGCCAGTCCTGCCTATGACAGGCGCCGCAGCCGCTC
GCCTGCAAGGGAAGATAGGGACTGAAGCTGTACCATGGATGGCTGCGCTCAATCCTGGGT
GCTTCGGACCAAATGGATGCACCGTCCTAGTGCGATGTTCGCTCAAGTTGGTTATGTTAG
GCAGCCAGGAACTTCTGTAATATCTCTCTATTAGCTAGCTCTAGCTGAATGCTTTGTCGA
TTTAGTTTGAACTGTGATTGTTAGCTTGAACTTTGTGCAAAGGGATTCTTCCGGTGAGAC
CATTTGCGGAGCGATGAGATGTACCGTGTATCGACCGACAGCAGTATTCTAGCTTTGCAC
TTTGGTTATTCTTCCATATGTTCCTATTCTTCACTATTGTTTCTGCTTGTGTGCTGGTCG
ACATGGTTGAGGATGGTGACCTTTGAGGAAGATAGAGGCTAATGTTGTGGTGGTGACGTC
CATGGCTTCGGCAACATACTTCTTCTGTACCTAAATAACTATAGTTCTTTTGTACCTAAA
TAGTTATAGTTGGGGAGAACTAGGTACTTCTGAAGTAGGAGAG



Protein Sequence (297 aa)

>BART1_0-u42531.007 297 150831_barley_pseudomolecules
MKIRSWLSGLGKICLYSNTNMRPIFCGNLDYDARQSEVERLFGKYGRVERVDMKTGFAFV
YMEDERDAEDAIRRLDRTDFGRTGRRLRVEWTKEDRSGGRKGNGKRSPSSVKPTKTLFVI
NFDPINTRTRDLEKHFDLYGKIANIRIRRNFAFVQYETQEDATKALDGTNGSTVMDRVIS
VEYALRDDDEKRNGYSPDRRGGRDRSPDRRDNRGRSASPYGRGRERGSPDYGRGRERGSP
DYGKGGARDSPDYVRGGSPYGGKGDDRASPKYDRERREASPAYDRRRSRSPAREDRD