Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u29974.007

ChromosomeExonStartStopDirection
chr4H1511456072511455881+
chr4H2511457260511457229+
chr4H3511457495511457384+
chr4H4511458147511457592+
chr4H5511459246511458277+


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
morexEMB10.346519.465517.9818
morexETI69.043852.768437.5781
morexLEA72.767891.1236101.072
morexEPI39.674950.58158.6066
morexROO30.738825.535316.0954
morexROO20.14854800.138171
morexNOD89.8358121.30245.746
morexRAC21.092720.56517.7615
morexINF17.2735114.629319.6255
morexINF277.656738.798768.861
morexCAR527.194116.08039.48272
morexCAR1525.531222.660329.5444
morexLEM53.839971.870534.7388
morexLOD49.378412.873783.9555
morexPAL37.821331.022744.8716
morexSEN51.0995130.826102.915



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os03g15890.2 +1 4e-42 156 71/81 (88%) protein|RNA recognition motif containing protein, expressed
TAIR PP10 AT1G07350 @ ARAPORT
AT1G07350.2 @ TAIR		 +1 5e-34 126 56/82 (68%) Symbols: | RNA-binding (RRM/RBD/RNP motifs) family protein | chr1:2258816-2259586 REVERSE LENGTH=129
BRACH PP3 Bradi1g67145.1.p +1 6e-45 163 76/81 (94%) pacid=32805382 transcript=Bradi1g67145.1 locus=Bradi1g67145 ID=Bradi1g67145.1.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 (1862 bp)

>BART1_0-u29974.007 1862 150831_barley_pseudomolecules
CCGGATTTGAGAAAGTCTCGCGTCCGGCCCTCTCCAGAACCTTCCGGCAGGTCCTCTCTA
TTTATTCACACGAGCGCGCGTGCACCATCCAACGGGAAAAGAGAGGCGGTGGTCGCAGGT
CGGAACTGACGGAGGCAGAGGCGAAGACGAAGACAGAGACTCGAGAGGCCTCGCAGCGGC
GACGAATCAAAGATGTCGTATTCGAGGTACAGGAGTCGTTCAAGGAGTGTGGACTCGAGT
GATGTTGAGAACCCTGGGAACAATCTCTTTGTGACTGGTTTATCATCTCGTCTAACTGAT
CGAGATCTGGAGAAGCATTTCTCTACAGAGGGAGAGGTGATTGATGCAAGTATTGTACTT
GATCCATGGACAAGGGAATCACGGGGATTTGGATTTGTTACCATGGCCAATCTTAAGGAG
GCAGAACGCTGCATCAAATATCTCGACAGTTCAGTGCTGGAAGGTCGTGTCATTACTGTT
GAGAAGGTATTGCCAAAAGATTGTTAACTCTGATATTTGTCCATTCTCCTTCTATATAGA
GTGGAACTATTATGTACAGATTAGCCTTCCAAGCTGAATATTTGAGTGCTCTTCTTGTTT
GAAGATTTTGTTGACAGCAGCAGGTTGATGCCCGCAGCTGTATGGCATCAAATTCAAAAG
ATACACAACCTAAGATCGAAACAATGCTACCTCAACCAAAGGGTTGTACGCCCACCGTTA
TTTTATTTTTCTGTATTATTTGTGTAGTTCAGATCCCCAATAATTTATCCAGTCTTGCTT
TTGACATAAAACACAATTACTGATTTGGAGCCCCCTTCTCCACCACAGGCAAAGAGAAGA
CGAGGTCGAACCCCAACACCGGGAAGGTACCTTGGCAGCAAATCATCGCGTCGAGGTATT
CCCGAAGCAGGTCACCTGTTAGGAGAGACCGTTACGGCTCACGCTACCCGCCCGAGCTAG
AACGTTCTTATTCTCCTTATCGCAGAGGACGATCATACTCTCGTCATGACAGGCATAGAT
CATACTCCCCCTATGGAAGGAGGCCATCCTACTCCCCCTATGAAAGGAGGCCATCCTACT
CTCCCTATGGCAGAAGGAGATCATACTCTCCTTCCGACAGGTCGGAGTCTCCCTACCACA
GGCGTAGATCCTACTCACCCTACGACAGGCGTCACTCACCCCGCTATGGTCATCGCCACC
GTTCAAGATCCCCATACAGTTACAGAAGGCGGAGGTCATGCTCCCATGACCGTTATGTTT
CAGCATACTACAGCAGGCGCTATTCTCCAAGGAACAGAAGACGGAGTTACTCTCGCAGCG
TATCACCACGCAGGAGCTACTCCCGTAGCTGCTCCCTGGCGTCAGAAGAATCAAGGAGCT
GTTCTCCGCAGAAAGGATATGCTGAAAGCAAGGCATCGCGCAGCAGGTCACCTGCGATTG
CGAAGAGGCGTTCTAGAGAAAGCTATGCGCACAGCCGCAGTTCATGCTCGAGGTCCGTCT
CCAGGGAGCGCTCAACCTCATCAAGCACCTGATGGTTTACAAAGTGCCTTGATGACTTTG
GATGTTTGTAAACAATGTGGATGGTATGATCGTGTACCTAGTGAAGCAGCTGTATTTCGT
CATCGTTAACATCTTAAATTGCAGTCTGCTTCCATACTATAGGAGAAAAATGCAGAAAAT
TTCCTACAGATTGCCTATTCCACAAGGATTTTATAGCATACTTCTACAACGGAAAAAACG
CAGAAATTTTCATAAATATTGGCGAGGTCATTTCTTTGTTTCAGATGACCCAGTGCGGAT
TTTTCTATAGGAATTCGATACTGCAATTTTCCTTTGTTTATAAGATCTCTAACTCAAACC
TC



Protein Sequence (104 aa)

>BART1_0-u29974.007 104 150831_barley_pseudomolecules
MSYSRYRSRSRSVDSSDVENPGNNLFVTGLSSRLTDRDLEKHFSTEGEVIDASIVLDPWT
RESRGFGFVTMANLKEAERCIKYLDSSVLEGRVITVEKVLPKDC