Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u05042.007

ChromosomeExonStartStopDirection
chr1H1501617123501616315-
chr1H2501617385501617276-
chr1H3501618080501617967-
chr1H4501618616501618447-
chr1H5501619174501618955-
chr1H6501619587501619330-


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
morexROO200.00000004136450
morexNOD000
morexRAC000
morexINF1000
morexINF2000
morexCAR500.4183050
morexCAR15000
morexLEM000
morexLOD000
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os08g06280.7 +3 2e-61 200 119/126 (94%) protein|LSD1 zinc finger domain containing protein, expressed
TAIR PP10 AT1G32540 @ ARAPORT
AT1G32540.1 @ TAIR		 +3 3e-53 179 105/125 (84%) Symbols: LOL1 | lsd one like 1 | chr1:11768253-11769591 FORWARD LENGTH=187
BRACH PP3 Bradi3g16400.3.p +3 1e-61 200 120/126 (95%) 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 (1681 bp)

>BART1_0-u05042.007 1681 150831_barley_pseudomolecules
GCTTTACCTTATCTGCCGCATTCCAACTCATGTTGTTATTCTGAGCAAAACTCGACTCGC
TCGCTCGTCTCGACATCTGCACCGGATCGAGCTCAGCAAAGCCCGAGCCGGAGGCGCTCG
TCTGCCCGGGGAGCGGCGCCATGCGGGTCCGCCTCTTCCTCTGAACCGGGCAAGCGCGAG
CCGCCTTCTTCCTCCGGCTCGGCGTCGGCGGCGACGACGAGCGTCGGTGGCGGCATAGCA
CGGTCCAGCGACGAGCAGAATCGCGGTGTTCTCACCGGAATCTCCCACAATTTATGCAGG
ATTTCATGTAGAGGAGGGCAATCTGTTCTCATCCCCTCGACTTCCAGCAGAGCGTGCGAA
GTCTCGTCCGCAGCAACGACGACGCCGGCTCAGGCAGCCGCGGGCACGGCAATGCCGGTT
CCTCTTGCCCCTTACCCAACTCCTCCTGCGCCCTTCACGCCACCCGCTCCCAATGCAGGT
GAGCTTCAGCCACTGAAATTTCATAACTAAGGTTCCATGCTTGAGCAATTTCAGGGGCTC
AAAGCCAACTTGTCTGCTCTGGGTGCCGGAATCTGCTCATGTATCCTGCCGGCGCAACGT
CGGTATGCTGCGCGGTTTGCAGTACCGTGACCGCTGTTCCGGCTCCTGGGACCGAGATGG
CGCAGCTAGTTTGCGGAGGATGCCACACTCTTCTGATGTACATACGTGGTGCCACAAGTG
TACAGTGTTCTTGCTGCCACACTGTCAACCTGGCAATGGAAGCGAATCAGGTTGCGCATG
TAAACTGTGGGAGTTGCCGAATGCTGCTCATGTACCAGTACGGCGCAAGGTCCGTCAAAT
GTGCAGTCTGCAGTTTCGTGACATCAGTTGGGGCATCATCGGGTGCAGAGCAGAAGCCCA
GCAACTGAAATCCTGCAAGTTCATTACGAAGGCAGCTTCCCGAAATAAGAATGCTTTGAG
TGCACATGTATAGAGTTCTTCCCAGAAGCAACCTTTTCCTCCCCTCTCCATTTCTCCCTT
CGTTGGACCTGGCGAGCTTGCGGAATAAACAAGAGTTTTTGGTAATACATAGTTGCTCAA
AATTCGTCGAATCATCTGTGTAACTGGGTCAGACAGATACATGAACCCACCATGTTTATG
TTCAAATTTAGCTTCTTTTACTTGTGTTCTATATATTTCAGATTTTTTTTCTTGTGGTCA
TCGGAAGAATTTCTTCAGATGTGCTTTGCCGTGCGTATTCTTGAACCGATCTATATCACT
GCAGACATGATCATGAACATGAACAGTTTACAAACACAGAAAAGTCCAAATGATGCATGG
TTAGGGTGTGCAAACACATCAGAGCTGATGTTGATTGCAAGGACACAGGATTGGGTGAGT
GTGGGGCACCATCTCTCTGATTCTTGCCCAACTCTGAATCTACAGCCGATGGCATGTCCC
AGCAAGCAAACAGCTTGTGGTGATCCGATGGCATGTCATGCATGATGCATCTGGTTTGAC
ACTGAGAAGGACTGTCAGTCCATGACCACTCTATCAATGCACACAATAATTGCAAGGAAA
GTTGTGCAGAAAGGTTTAGAGAACACAATGATGTAAAGGCAGGCATAGATGGCGCTCAGT
CGCGTCAGCACTCAGTGCTAGTAACAGCTCAGAAACATACTCGTACTACTGAACAGCAGC
A



Protein Sequence (122 aa)

>BART1_0-u05042.007 122 150831_barley_pseudomolecules
MLRGLQYRDRCSGSWDRDGAASLRRMPHSSDVHTWCHKCTVFLLPHCQPGNGSESGCACK
LWELPNAAHVPVRRKVRQMCSLQFRDISWGIIGCRAEAQQLKSCKFITKAASRNKNALSA
HV