Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u05042.001

ChromosomeExonStartStopDirection
chr1H1501617123501616289-
chr1H2501617385501617276-
chr1H3501618080501617967-
chr1H4501618560501618447-
chr1H5501619133501618955-
chr1H6501619865501619330-


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
morexEPI000
morexROO000
morexROO2000
morexNOD0.81121800
morexRAC000
morexINF10.00041332500
morexINF2000
morexCAR5000.977216
morexCAR15000
morexLEM000
morexLOD000
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os08g06280.7 +1 1e-59 196 117/123 (95%) protein|LSD1 zinc finger domain containing protein, expressed
TAIR PP10 AT1G32540 @ ARAPORT
AT1G32540.3 @ TAIR		 +1 6e-53 178 105/122 (86%) Symbols: LOL1 | lsd one like 1 | chr1:11768043-11769591 FORWARD LENGTH=154
BRACH PP3 Bradi3g16400.3.p +1 7e-60 197 118/123 (96%) pacid=32812785 transcript=Bradi3g16400.3 locus=Bradi3g16400 ID=Bradi3g16400.3.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 (1888 bp)

>BART1_0-u05042.001 1888 150831_barley_pseudomolecules
ATAAATTTTCACAGCGAACCGTTTGTAACTCGGGAAATGACAAGAATTCTTATTAGAGTA
GCTAACATGATGATGTACATGCTAATCCTAGTGTTTTTTTTCGCTTCTTTTCATTCCAAA
ACCACATGTTGCTGCACAGGATTGTTGACGGAGATTTCTATAAACGAAAACGAAAGCAAA
AAAAATTACACAGAACAGGATAGCGTAGTGAGTTTCGACGGGGCCCACATGGCATAGGGG
ATAAGAAAGAGAATCCACGTTCCCAGCCACAGTGCCGTGCTTTACCTTATCTGCCGCATT
CCAACTCATGTTGTTATTCTGAGCAAAACTCGACTCGCTCGCTCGTCTCGACATCTGCAC
CGGATCGAGCTCAGCAAAGCCCGAGCCGGAGGCGCTCGTCTGCCCGGGGAGCGGCGCCAT
GCGGGTCCGCCTCTTCCTCTGAACCGGGCAAGCGCGAGCCGCCTTCTTCCTCCGGCTCGG
CGTCGGCGGCGACGACGAGCGTCGGTGGCGGCATAGCACGGTCCAGCGACGAGCAGGATT
TCATGTAGAGGAGGGCAATCTGTTCTCATCCCCTCGACTTCCAGCAGAGCGTGCGAAGTC
TCGTCCGCAGCAACGACGACGCCGGCTCAGGCAGCCGCGGGCACGGCAATGCCGGTTCCT
CTTGCCCCTTACCCAACTCCTCCTGCGCCCTTCACGCCACCCGCTCCCAATGCAGGGGCT
CAAAGCCAACTTGTCTGCTCTGGGTGCCGGAATCTGCTCATGTATCCTGCCGGCGCAACG
TCGGTATGCTGCGCGGTTTGCAGTACCGTGACCGCTGTTCCGGCTCCTGGGACCGAGATG
GCGCAGCTAGTTTGCGGAGGATGCCACACTCTTCTGATGTACATACGTGGTGCCACAAGT
GTACAGTGTTCTTGCTGCCACACTGTCAACCTGGCAATGGAAGCGAATCAGGTTGCGCAT
GTAAACTGTGGGAGTTGCCGAATGCTGCTCATGTACCAGTACGGCGCAAGGTCCGTCAAA
TGTGCAGTCTGCAGTTTCGTGACATCAGTTGGGGCATCATCGGGTGCAGAGCAGAAGCCC
AGCAACTGAAATCCTGCAAGTTCATTACGAAGGCAGCTTCCCGAAATAAGAATGCTTTGA
GTGCACATGTATAGAGTTCTTCCCAGAAGCAACCTTTTCCTCCCCTCTCCATTTCTCCCT
TCGTTGGACCTGGCGAGCTTGCGGAATAAACAAGAGTTTTTGGTAATACATAGTTGCTCA
AAATTCGTCGAATCATCTGTGTAACTGGGTCAGACAGATACATGAACCCACCATGTTTAT
GTTCAAATTTAGCTTCTTTTACTTGTGTTCTATATATTTCAGATTTTTTTTCTTGTGGTC
ATCGGAAGAATTTCTTCAGATGTGCTTTGCCGTGCGTATTCTTGAACCGATCTATATCAC
TGCAGACATGATCATGAACATGAACAGTTTACAAACACAGAAAAGTCCAAATGATGCATG
GTTAGGGTGTGCAAACACATCAGAGCTGATGTTGATTGCAAGGACACAGGATTGGGTGAG
TGTGGGGCACCATCTCTCTGATTCTTGCCCAACTCTGAATCTACAGCCGATGGCATGTCC
CAGCAAGCAAACAGCTTGTGGTGATCCGATGGCATGTCATGCATGATGCATCTGGTTTGA
CACTGAGAAGGACTGTCAGTCCATGACCACTCTATCAATGCACACAATAATTGCAAGGAA
AGTTGTGCAGAAAGGTTTAGAGAACACAATGATGTAAAGGCAGGCATAGATGGCGCTCAG
TCGCGTCAGCACTCAGTGCTAGTAACAGCTCAGAAACATACTCGTACTACTGAACAGCAG
CATCACTATTCATGTGTTTTTTCCTGTT



Protein Sequence (122 aa)

>BART1_0-u05042.001 122 150831_barley_pseudomolecules
MLRGLQYRDRCSGSWDRDGAASLRRMPHSSDVHTWCHKCTVFLLPHCQPGNGSESGCACK
LWELPNAAHVPVRRKVRQMCSLQFRDISWGIIGCRAEAQQLKSCKFITKAASRNKNALSA
HV