Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u30598.011

ChromosomeExonStartStopDirection
chr4H1574820351574820336+
chr4H2574820541574820449+
chr4H3574820930574820755+
chr4H4574821065574821019+
chr4H5574822272574822203+
chr4H6574822810574822584+
chr4H7574822997574822908+
chr4H8574823189574823114+
chr4H9574823585574823332+
chr4H10574826248574826090+


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
morexETI00.461920
morexLEA2.310100.0000000436834
morexEPI000.0283833
morexROO00.6069451.67322
morexROO200.3264680
morexNOD000
morexRAC000.509819
morexINF16.038652.211930
morexINF20.00000008674312.821396.15507
morexCAR50.6393435.860680
morexCAR150.133690.0002051180
morexLEM0.32354200
morexLOD000.851183
morexPAL0.4247230.9496320.526633
morexSEN0.3505630.2482930.452026



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os03g10460.1 +3 5e-172 486 245/311 (79%) protein|expressed protein
TAIR PP10 AT2G18410 @ ARAPORT
AT2G18410.1 @ TAIR		 +3 4e-72 230 129/313 (41%) 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 +3 0.0 539 265/311 (85%) 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 (1208 bp)

>BART1_0-u30598.011 1208 150831_barley_pseudomolecules
GGAAGGCGCAGGCCAGGGGACTTGTGGTTGTGGCGTTTGACCGGAGCCCGGAAGTTTACC
TGGATGCCATGCTTCGGCACGGCCTTGATTCGAATGCACTGAGTCGATGTGTTCGGATAT
TGGATTGCTACTCAGACCCACTCGGGTGGAAGAAAAATATCCGAAGTCAGCAGCATCATG
AGGACAGTGGAACACCGTGCTCATCAAACAAAGGCAACATCACAATTTTCAGAAGCGTGA
AGGATGTTGATAAGTTATCGTGCTCCATAATTGATCTTGGAAGAGGGTTTGAAGGAGAAG
GCAAGACCTATTTTTCTGTTGCTCTCGATTCAATTAGCTCTATGTTAAGGCATGCTTCAG
TGCAATCAATTTCAGGCCTTCTTAGTAATCTTCGGAGCCATGATCAGATATCATCAATCT
TCTGGCTAATGCATTCAGATCTCCATGAAACCAAGTTTTCCCGAGCTTTTGAATGCCTTT
CTACCATGGTTGCTTGTGTAGAGCCAGAAGTTGTAGATTCTGTATATGGAGAAGAACGTA
GGGGGGACATGTCTTTCCTTGAGCATAACTATTCGAAAGCAAAGTTCCATGTGCGCCTGA
AACGAAGGAATGGACGGGTGAAGCATCTGCATGAGGAGTTATGTGTTGAGGGATATGATG
TAAAATTTGTTTCTGCTACTTCTGTAAGTATGGAAGTGAACCAAAGTCTACTACCTAAGG
TTCAGTTCAATCTTGAGCTGTCAGAAAAGGAACGGAGTGACAGGGCAAATGTTGTTCTTC
CTTTCGAACATCAAGGAAAGGGCGAGCCAATCCGTATATATGATGGACGGCGATCTCTCC
CGGAGGCTCGTCAAGATCTCAATTTTACTACGGCAGCTCTCCTGGATGAAACAGAAGCTC
TTAAATCTGCAGACACGAAGGGTGAAATTCATTACCTTCGTGATTCTGATGATGAGCGAC
CTGACTCGGATGAAGACCCCGATGATGATTTGGATATTTAGCCACAATGTGAGCTCTGTT
TATCCTAGTGGTCAGCTATCAAGTCAAAGGATCGCAAAAGACGGGGTTCTGGAGACCTGC
TCTCCCGTACAGCCATGCATGTAGTTGACGGGATAGGATCGCCGGAAGCAACGGTAGCGA
GCGAAACAACGGCGGGTTGTGCGCGAGGAGGTAGAGCAGATGCGATTTGATATGGGTCAC
GGCTAGGG



Protein Sequence (332 aa)

>BART1_0-u30598.011 332 150831_barley_pseudomolecules
KAQARGLVVVAFDRSPEVYLDAMLRHGLDSNALSRCVRILDCYSDPLGWKKNIRSQQHHE
DSGTPCSSNKGNITIFRSVKDVDKLSCSIIDLGRGFEGEGKTYFSVALDSISSMLRHASV
QSISGLLSNLRSHDQISSIFWLMHSDLHETKFSRAFECLSTMVACVEPEVVDSVYGEERR
GDMSFLEHNYSKAKFHVRLKRRNGRVKHLHEELCVEGYDVKFVSATSVSMEVNQSLLPKV
QFNLELSEKERSDRANVVLPFEHQGKGEPIRIYDGRRSLPEARQDLNFTTAALLDETEAL
KSADTKGEIHYLRDSDDERPDSDEDPDDDLDI