Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u30598.002

ChromosomeExonStartStopDirection
chr4H1574820351574819324+
chr4H2574820541574820449+
chr4H3574820930574820755+
chr4H4574821065574821019+
chr4H5574822272574822203+
chr4H6574822810574822584+
chr4H7574822997574822908+
chr4H8574823189574823114+
chr4H9574823585574823332+
chr4H10574827612574827520+
chr4H11574829588574828831+


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
morexEMB00.07429430
morexETI000
morexLEA00.1871680
morexEPI000.0653027
morexROO0.16333800
morexROO2000.0830027
morexNOD0.072724500.101408
morexRAC000
morexINF100.1654090
morexINF20.07093330.2184990.292994
morexCAR50.0859870.04743380
morexCAR15000
morexLEM000
morexLOD000
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os03g10460.1 +1 2e-179 526 289/363 (80%) protein|expressed protein
TAIR PP10 AT2G18410 @ ARAPORT
AT2G18410.1 @ TAIR		 +1 1e-72 244 147/365 (40%) Symbols: | FUNCTIONS IN: molecular_function unknown; INVOLVED IN: biological_process unknown; LOCATED IN: cellular_component unknown; EXPRESSED IN: 22 plant structures; EXPRESSED DURING: 13 growth stages; CONTAINS InterPro DOMAIN/s: Histone acetylation protein 2 (InterPro:IPR019519); Has 35333 Blast hits to 34131 proteins in 2444 species: Archae - 798; Bacteria - 22429; Metazoa - 974; Fungi - 991; Plants - 531; Viruses - 0; Other Eukaryotes - 9610 (source: NCBI BLink). | chr2:7990768-7992588 FORWARD LENGTH=374
BRACH PP3 Bradi1g71057.2.p +1 0.0 594 312/363 (86%) pacid=32795801 transcript=Bradi1g71057.2 locus=Bradi1g71057 ID=Bradi1g71057.2.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 (2912 bp)

>BART1_0-u30598.002 2912 150831_barley_pseudomolecules
CCCAAACACATAGCTTTCATGTGCCCCAATAAAGGAATTTCAATAAGCATCTGACAGTTG
CCAAAAAAAAAAAAAAGAGGAACAACAGACAATTATGTCTGAAAAAAGACAGTTAGGAGC
AAGTAGTTGCCCCTACGAGGATTCCATAACAGCTCAACCAAATTAACAGATACTAGTTCT
CATGTGCTAAATAAAAGGGATTTCAGTGAATAACAGGCAATATACTATCACAAGTAAGCT
AGAAAAGAATTTGCAGAAACAACATATACTAATCTTTATAGCAAGTCCGAGCAATCATGT
CGATTCAAATGAATTATGTGATTGCAGGGATGCAACTGCAAGTAGCAATACGAAACTCAG
TGCCATGGGAACAACAAGCCGTCTAGCAAATTTCTTGGCAAGCGGGGGCATCAATTAGGG
GGGCAAACGGACAGGAACCACAGAGACGAAGAGAGATACTGTACCTCTGAGCCAGCGGCT
GCCTGGCGGGGGCGCGAACCAGCGGGAGCCTCTCCCCCGCCGCCCTCGCGCACGCCTGCA
TCTTCCCCGCTCTCCTCTTCTTCCCTCCTCTCGCCGCCGTCGCCGCCGCCGTCGCCGCCG
CGCAGGAAACGAGCAGAGGAACCGGAGAAGCCGGGCTTAGAACAGGGAGGAGGAGTCAAA
CGTATCCGACATGGAAAGGGGGAGGCCGCACTCCGAGTCTGCCTGACAGGTGGGACCCAC
GCCGCTCCTGAGTCCCGACTTCCGGGAGCTCTGCGAAAGAGGCCAGAGGGGCTCTTGTGC
AAAAGCTCCACCCTCTCGCGCTAGGGTTTAAGGTTCTGAGTCGGGAGGCGCCGCCGGCGA
CGACGACGGGGAGCTGAGATGGCGGACGCGGCCGTGAGGTGCCTCCGGGACGGCCGCCTC
GACGGCGAGCACGCGCCAGCGCTGGCCGTGGAGGGCTCCCTCCAGTGCTGCCCCCTCGCG
GCGCGCGCCATGCTCCACGTCGCCGCCGCCGTCGCCTCCAACGCGGCCGCGGGGAAGGCG
CAGGCCAGGGGACTTGTGGTTGTGGCGTTTGACCGGAGCCCGGAAGTTTACCTGGATGCC
ATGCTTCGGCACGGCCTTGATTCGAATGCACTGAGTCGATGTGTTCGGATATTGGATTGC
TACTCAGACCCACTCGGGTGGAAGAAAAATATCCGAAGTCAGCAGCATCATGAGGACAGT
GGAACACCGTGCTCATCAAACAAAGGCAACATCACAATTTTCAGAAGCGTGAAGGATGTT
GATAAGTTATCGTGCTCCATAATTGATCTTGGAAGAGGGTTTGAAGGAGAAGGCAAGACC
TATTTTTCTGTTGCTCTCGATTCAATTAGCTCTATGTTAAGGCATGCTTCAGTGCAATCA
ATTTCAGGCCTTCTTAGTAATCTTCGGAGCCATGATCAGATATCATCAATCTTCTGGCTA
ATGCATTCAGATCTCCATGAAACCAAGTTTTCCCGAGCTTTTGAATGCCTTTCTACCATG
GTTGCTTGTGTAGAGCCAGAAGTTGTAGATTCTGTATATGGAGAAGAACGTAGGGGGGAC
ATGTCTTTCCTTGAGCATAACTATTCGAAAGCAAAGTTCCATGTGCGCCTGAAACGAAGG
AATGGACGGGTGAAGCATCTGCATGAGGAGTTATGTGTTGAGGGATATGATGTAAAATTT
GTTTCTGCTACTTCTGTAAGTATGGAAGTGAACCAAAGTCTACTACCTAAGGTTCAGTTC
AATCTTGAGCTGTCAGAAAAGGAACGGAGTGACAGGGCAAATGTTGTTCTTCCTTTCGAA
CATCAAGGAAAGGGCGAGCCAATCCGTATATATGATGGACGGCGATCTCTCCCGGAGGCT
CGTCAAGATCTCAATTTTACTACGGCAGCTCTCCTGGATGAAACAGAAGCTCTTAAATCT
GCAGACACGAAGGGTGAAATTCATTACCTTCGTGATTCTGATGATGAGCGACCTGACTCG
GATGAAGACCCCGATGATGATTTGGATATTTAGCCACAATGTGAGCTCTGTTTATCCTAG
TGGTCAGCTATCAAGTCAAAGATCCTCTTCAACGACTCCAACCAACAACGTGGTCAAATA
CGAGACTCTCATTCATGGTTTGCGTTTGGCCATCTCCATGGGCATTCACAAGAGGAACAT
CAGGCGCTTGCGAAAATTCTAGGAGGCGTTCACTTTGCGTGGGCGGCTGGAGCTACTGCA
TAGTTATGGTTGAACAATTTAAGCACCTGTATTATGTATAGCTTCGTGAGCATTGGAAGG
CAACCTTTGCAAATCACTGGGTTTGAAATTTCTTGGATGCTCAAGACTAATGTGTTGATG
GTAGCATATCGAATGAAAGGTCATATGCCCCAATGCGATTTTGTAGTTTTGTTTCGACGT
GGATGAATGTTGGCTAGTGTGTCAGTCGCTGAAATGGGTCCAGAACAAGAGGATGCGACA
TGTAACACTGTTTTTTCAGTTATATGAGAATATACACCGGGCTATTTGTTTGCTGGATGC
TTACTTCTGTTCATTAATGTTTGATGGCTAGTAGTAACTGATTGTTCAGCCTTTGGTGAA
TTTCCATTAACTAAACCAGCGTTAAACGCGTGACATGCTTCATTTTACTGTCGTATAGAG
GATGGCAGAAATGACATGCAAACTTGTACTGTATATTAAGAAGAACAAATAGAACTTCTT
CATTCATAATTTATAAATTGAACATATGATCCATCGCCTCTCCAGGACTGAGAACTCAAT
CTCATGGGCGGGCGCCAATGAAATCCCAACAACAATGCTCTAAATCAACAACAATCAATG
GCAGGCATATCTGAAATCACCGTATGGGCGCTAGCTAGACGCCTATGCATGCTAGTACCA
GTATTAGACTAGACGTGTATGGTGTACTCGTC



Protein Sequence (384 aa)

>BART1_0-u30598.002 384 150831_barley_pseudomolecules
MADAAVRCLRDGRLDGEHAPALAVEGSLQCCPLAARAMLHVAAAVASNAAAGKAQARGLV
VVAFDRSPEVYLDAMLRHGLDSNALSRCVRILDCYSDPLGWKKNIRSQQHHEDSGTPCSS
NKGNITIFRSVKDVDKLSCSIIDLGRGFEGEGKTYFSVALDSISSMLRHASVQSISGLLS
NLRSHDQISSIFWLMHSDLHETKFSRAFECLSTMVACVEPEVVDSVYGEERRGDMSFLEH
NYSKAKFHVRLKRRNGRVKHLHEELCVEGYDVKFVSATSVSMEVNQSLLPKVQFNLELSE
KERSDRANVVLPFEHQGKGEPIRIYDGRRSLPEARQDLNFTTAALLDETEALKSADTKGE
IHYLRDSDDERPDSDEDPDDDLDI