Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u25435.024

ChromosomeExonStartStopDirection
chr3H1681733477681733145-
chr3H2681734115681733967-
chr3H3681734573681734396-
chr3H4681735055681734986-
chr3H5681735974681735231-
chr3H6681736144681736050-
chr3H7681736609681736477-
chr3H8681737010681736954-
chr3H9681737704681737606-
chr3H10681737948681737800-
chr3H11681738516681738306-
chr3H12681738721681738587-
chr3H13681738879681738807-
chr3H14681739133681738961-
chr3H15681739956681739754-


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
morexEMB0.5820370.5275522.06015
morexETI2.119311.618271.06055
morexLEA00.6408310
morexEPI0.972172.888231.29659
morexROO0.09959620.2806050.417191
morexROO22.058421.823831.14758
morexNOD0.000001725960.7058132.45065
morexRAC2.721631.81391.95314
morexINF101.817861.17442
morexINF26.223823.272416.12555
morexCAR53.004290.4264120
morexCAR1500.5942950.83036
morexLEM1.468971.515681.44121
morexLOD2.541213.757620.806289
morexPAL1.531061.497141.77476
morexSEN3.962813.084332.95158



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os01g72880.1 +3 0.0 647 324/366 (89%) protein|DNA mismatch repair protein Mlh1, putative, expressed
TAIR PP10 AT4G09140 @ ARAPORT
AT4G09140.1 @ TAIR		 +3 3e-179 537 266/367 (72%) Symbols: ATMLH1, MLH1 | MUTL-homologue 1 | chr4:5817107-5821035 REVERSE LENGTH=737
BRACH PP3 Bradi2g61370.2.p +3 0.0 677 340/366 (93%) pacid=32771965 transcript=Bradi2g61370.2 locus=Bradi2g61370 ID=Bradi2g61370.2.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 (2802 bp)

>BART1_0-u25435.024 2802 150831_barley_pseudomolecules
GCGGGGAGCCGCCCCGCATCCGGCGGCTGGAGGAGTCGGTGGTGAACCGCATCGCCGCGG
GGGAGGTGATCCAGCGGCCCTCGTCGGCGGTGAAGGAACTCGTCGAGAACAGCATCGACG
CCGGCTCCTCCACCATCTCCGTCACCGTCAAGGACGGGGGCCTCAAGCTCATCCAGGTCT
CGGACGACGGCCACGGCATCCGGTGTGAGGACTTGCCAATATTGTGTGAGAGGCATACTA
CCTCAAAGTTGTCTGCATATGAGGATCTACAGACAATAAAGTCCATGGGGTTCAGAGGGG
AGGCTTTGGCCAGTATGACTTATGTTGGCCATGTTACCGTGACAACAATAACAGAAGGCC
AACTGCATGGCTACAGAGTTTCTTATAGGGATGGAGTAATGGAGAATGACCCAAAGCCCT
GTGCTGCGGTTAAAGGAACTCAAATCATGGTTGAAAATTTATTCTACAATATGGTAGCTC
GTAGGAAAACACTGCAGAACTCCAATGATGACTATCCAAAGATAGTGGACTTCATCAGTC
GGTTTGCAGTCCATCACATCAATGTGAACTTCTCTTGCAGAAAGCATGGAGCCAATAGAG
CAGATGTTCACAGTGGGAGCACATCTTCAAGGCTAGATGCTATCAGGAATGTCTATGGGG
CTTCGGTTGTTCGTGATCTGATGGAAATACAGGTTTCAGATGAGAATGCTGTAGATGAAA
TATTCAAGATGGATGGTTTCATCTCAAATGCAAATTATGTGGCAAAGAAGACTACTATGA
TTCTTTTCATAAATGATCGACTTGTAGATTGCACTTCTTTGAAAAGAGCTACTGAATTTG
TGTACTCTGCAATACTGCCTCAAGCATCGAAACCCTTCATATACATGTCCATCAATCTTC
CACCAGAACACGTGGATGTCAATATACATCCAACCAAAAAGGAGGTTAGCCTCTTAAATC
AAGAGCGTATTATTGAAAAAATTAAAGATGCCATCGAGGAAAAACTGGTGAACTGTAATA
ACACAAGGATATTCCAAACTCAGGCACTAAACCCTTCAGCACTTACTCAAGCTAACACAC
GAAAGGACATGGGTACCGAGGAGAAAAATCTCAAAAGATTCCTGTGAGCCAAATTGTCAG
AACAGATCCTCGCGATCCATCTGGAAGGTTGCACACCTATTGGCAAGGTCAAACTTCAAA
TCTTGAAAAGAAGTCTGACCTTGTTGCCGTAAGAAATATTGTAAGATCAAGAAGGAATCC
AAAAGATGCTGGTGATTTGTCCAGTCGCCATGAGCTTGTTACAGAAATAGATTCTAACTT
ACATCCTGGCCTTTTCGATATTGTTAAGAATTGCACATATGTTGGAGTTGCGGATGAAGT
TTTCGCTTTGATACAACACAATACCCTCTTATACCTTGTCAATGTGGTAAATGTTAGGTA
AACTCTATACAGTACATTGATGACTAGTCATACTCTTCTATGCTTTGTATCTCTTATTTA
AGCTAGATTTTTTCTTCTAACATCTGACATAGTTATTTGAAGGTAACCGATACCCCAGTT
ACCTGTACATATTTGCAAATGCACGCGCACACAAACAATATTGCTTGCACACACCACCAT
CAAACTGCTATCCATTCACATCGCATCCAGTTGAACGCCTGCAACTGCTAAATAATAAGC
ACCTCTTCCAAATATTGCATTGTTTTCTTTTCTGTACCACTCCCTCTGTTTCTAAATATA
AGTCTTTTTAAAGATTTCACTAGGGGACTACATACAGAGCAAAATGAGTGAATCTATACT
CTAATATATGTATATATACATCCGTATGTAGTTTTCTAGTGGAAATTCTAAAAAGACTTA
TATTTAGGAACGAAGGGAGTATATGATATTGATGATTCAGCTTGTGATGCAGCAAAGAAC
TCATGTACCAACAAGCCTTGTGCCGTTTTGGGAACTTCAATGCTATAAAACTCAGTGAAC
CAGCTCCACTTCTGGAGTTGCTGAGAATGGCACTGAAAGATGACGAGTCAATGAGTGATG
TAAATGAGAAGGAGAAACTAGAAATTGCAGAAGTGAACACTGAGATACTGAAAGAAAATG
CTGAGATGATTAATGAGTACTTCTCTATTCACATTGATCAAGATTACCTGGGACGTTGAG
AAAGAGTGCTTCAGAACGGCAGCAGCTGCTATCGGAAACTTCTATGCGCTTCATCCTCCC
ATCCTTCCAAATCCATCTGGCAAAGGCATTCAGTTATACAAGAAAAATAAAGATTGCATG
GGAAGTGCTGAACAGGCTGATAACAATTTACCAAGTACAGATGAAGATGACATCGATCAA
GAGCTGCTTGCGGAAGCAGAGGCAGCATGGGCTCAACGTGAGTGGACCATCCAGCACGTC
TTGTTCCCGTCGATGCGACTTTTCCTCAAGCCCCCTAAGTCGATGGCAACTGATGGAACG
TTTGTCCAGATTGCTTCTCTAGACAAGCTTTACAAGATCTTCGAGAGATGCTAGCCGACA
AGCGGCATGTCGAGAAGGAAGGGAAGAGCGCGACGCGACCGACGCCCTTGCCGGTTCCTT
CCGGGACGTGTGTATATAATGCGGTGTCACTGTTTTTTCCCCCCTTTTTCCGATAGGGCT
GTAAATATTTTTGAAGGACGAGCAAAGTTTGCTGGGCTCCAGCTCAGCCCTGGAATTGAA
TGGCAAATGCACGAATGATTTGGCTCTGCTACGCAATGCTGTCATTGTTGTTTCCCTCTA
ATGACCCCGCTGGCAGATATGTCATGCCCTCTTACAACGATC



Protein Sequence (374 aa)

>BART1_0-u25435.024 374 150831_barley_pseudomolecules
GEPPRIRRLEESVVNRIAAGEVIQRPSSAVKELVENSIDAGSSTISVTVKDGGLKLIQVS
DDGHGIRCEDLPILCERHTTSKLSAYEDLQTIKSMGFRGEALASMTYVGHVTVTTITEGQ
LHGYRVSYRDGVMENDPKPCAAVKGTQIMVENLFYNMVARRKTLQNSNDDYPKIVDFISR
FAVHHINVNFSCRKHGANRADVHSGSTSSRLDAIRNVYGASVVRDLMEIQVSDENAVDEI
FKMDGFISNANYVAKKTTMILFINDRLVDCTSLKRATEFVYSAILPQASKPFIYMSINLP
PEHVDVNIHPTKKEVSLLNQERIIEKIKDAIEEKLVNCNNTRIFQTQALNPSALTQANTR
KDMGTEEKNLKRFL