Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u05042.002

ChromosomeExonStartStopDirection
chr1H1501617123501616289-
chr1H2501617385501617276-
chr1H3501618616501617967-
chr1H4501619133501618955-
chr1H5501619618501619330-


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
morexEMB000
morexETI000
morexLEA000
morexEPI00.09756740
morexROO000
morexROO2000.0000000210074
morexNOD000.00000000507441
morexRAC000
morexINF1000
morexINF2000
morexCAR5000
morexCAR15000
morexLEM0.3742390.5118150
morexLOD000
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os08g06280.7 +2 4e-48 167 81/88 (92%) protein|LSD1 zinc finger domain containing protein, expressed
TAIR PP10 AT1G32540 @ ARAPORT
AT1G32540.1 @ TAIR		 +2 1e-42 152 75/92 (82%) Symbols: LOL1 | lsd one like 1 | chr1:11768253-11769591 FORWARD LENGTH=187
BRACH PP3 Bradi3g16400.5.p +2 5e-49 167 83/88 (94%) pacid=32812787 transcript=Bradi3g16400.5 locus=Bradi3g16400 ID=Bradi3g16400.5.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 (2063 bp)

>BART1_0-u05042.002 2063 150831_barley_pseudomolecules
AGAGAATCCACGTTCCCAGCCACAGTGCCGTGCTTTACCTTATCTGCCGCATTCCAACTC
ATGTTGTTATTCTGAGCAAAACTCGACTCGCTCGCTCGTCTCGACATCTGCACCGGATCG
AGCTCAGCAAAGCCCGAGCCGGAGGCGCTCGTCTGCCCGGGGAGCGGCGCCATGCGGGTC
CGCCTCTTCCTCTGAACCGGGCAAGCGCGAGCCGCCTTCTTCCTCCGGCTCGGCGTCGGC
GGCGACGACGAGCGTCGGTGGCGGCATAGCACGGTCCAGCGACGAGCAGGATTTCATGTA
GAGGAGGGCAATCTGTTCTCATCCCCTCGACTTCCAGCAGAGCGTGCGAAGTCTCGTCCG
CAGCAACGACGACGCCGGCTCAGGCAGCCGCGGGCACGGCAATGCCGGTTCCTCTTGCCC
CTTACCCAACTCCTCCTGCGCCCTTCACGCCACCCGCTCCCAATGCAGGTGAGCTTCAGC
CACTGAAATTTCATAACTAAGGTTCCATGCTTGAGCAATTTCAGGGGCTCAAAGCCAACT
TGTCTGCTCTGGGTGCCGGAATCTGCTCATGTATCCTGCCGGCGCAACGTCGGTATGCTG
CGCGGTTTGCAGTACCGTGACCGCTGTTCCGGCTCCTGGTATGCACATCAATCTCATTTT
GCCCATCAAGGATTTGTATGCAATGTGGCAGCCACTGAACATTGAGTTCCATATCTGCAT
GATTAGTATGGGAGACAGCAGTGTGCATTCTAATCGACTCTGACAAGTAACATCCTTTGT
TATTTTTAATGAAAAGAAACGCAACATCTCGTTTATCTGTGCACTTAACTTCTGAAGTTT
ACCAAGAAAGGACGATTTTGCATGCATATTTCACCACACTTGCAGATCAAGGGGGTTAAA
AATGTAACCCCTTAAACCAATCCAATCCAAAACGCTTTGCATTAGCTGGAAACTATCCTG
AAGTGCGGTTCTCTGAATGTATTTTCCACCCTGATTCGGTGCAGGGACCGAGATGGCGCA
GCTAGTTTGCGGAGGATGCCACACTCTTCTGATGTACATACGTGGTGCCACAAGTGTACA
GTGTTCTTGCTGCCACACTGTCAACCTGGCAATGGAAGCGAATCAGGTTGCGCATGTAAA
CTGTGGGAGTTGCCGAATGCTGCTCATGTACCAGTACGGCGCAAGGTCCGTCAAATGTGC
AGTCTGCAGTTTCGTGACATCAGTTGGGGCATCATCGGGTGCAGAGCAGAAGCCCAGCAA
CTGAAATCCTGCAAGTTCATTACGAAGGCAGCTTCCCGAAATAAGAATGCTTTGAGTGCA
CATGTATAGAGTTCTTCCCAGAAGCAACCTTTTCCTCCCCTCTCCATTTCTCCCTTCGTT
GGACCTGGCGAGCTTGCGGAATAAACAAGAGTTTTTGGTAATACATAGTTGCTCAAAATT
CGTCGAATCATCTGTGTAACTGGGTCAGACAGATACATGAACCCACCATGTTTATGTTCA
AATTTAGCTTCTTTTACTTGTGTTCTATATATTTCAGATTTTTTTTCTTGTGGTCATCGG
AAGAATTTCTTCAGATGTGCTTTGCCGTGCGTATTCTTGAACCGATCTATATCACTGCAG
ACATGATCATGAACATGAACAGTTTACAAACACAGAAAAGTCCAAATGATGCATGGTTAG
GGTGTGCAAACACATCAGAGCTGATGTTGATTGCAAGGACACAGGATTGGGTGAGTGTGG
GGCACCATCTCTCTGATTCTTGCCCAACTCTGAATCTACAGCCGATGGCATGTCCCAGCA
AGCAAACAGCTTGTGGTGATCCGATGGCATGTCATGCATGATGCATCTGGTTTGACACTG
AGAAGGACTGTCAGTCCATGACCACTCTATCAATGCACACAATAATTGCAAGGAAAGTTG
TGCAGAAAGGTTTAGAGAACACAATGATGTAAAGGCAGGCATAGATGGCGCTCAGTCGCG
TCAGCACTCAGTGCTAGTAACAGCTCAGAAACATACTCGTACTACTGAACAGCAGCATCA
CTATTCATGTGTTTTTTCCTGTT



Protein Sequence (111 aa)

>BART1_0-u05042.002 111 150831_barley_pseudomolecules
MPAFTSLCSLNLSAQLSLQLLCALIEWSWTDSPSQCQTRCIMHDMPSDHHKLFACWDMPS
AVDSELGKNQRDGAPHSPNPVSLQSTSALMCLHTLTMHHLDFSVFVNCSCS