Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u25435.022

ChromosomeExonStartStopDirection
chr3H1681728097681727737-
chr3H2681728628681728591-
chr3H3681728833681728758-
chr3H4681729057681728926-
chr3H5681729385681729308-
chr3H6681729697681729472-
chr3H7681730185681729865-
chr3H8681730317681730271-
chr3H9681730783681730695-
chr3H10681731206681731096-
chr3H11681732673681732395-


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
morexROO2000.238339
morexNOD000
morexRAC000
morexINF1000
morexINF2000
morexCAR5000
morexCAR15000
morexLEM000
morexLOD0.37781700
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os01g72890.2 +2 1e-35 139 64/92 (70%) protein|transposon protein, putative, CACTA, En/Spm sub-class, expressed
TAIR PP10None-----
BRACH PP3 Bradi2g61380.4.p +2 6e-35 137 66/87 (76%) pacid=32777636 transcript=Bradi2g61380.4 locus=Bradi2g61380 ID=Bradi2g61380.4.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 (1758 bp)

>BART1_0-u25435.022 1758 150831_barley_pseudomolecules
CGCCCCCGTCCTCCTTCACCCCATCCATATCCCCCCCGACCAAAACCCTAGCTCGCGCTC
CAGACCCCGCACGCCCGCCGCCGCCGCGGGGAGACGGACGACGATGGCGAAGCCCCGCCG
CGGCCGCTCAGGCTCGCGGTCCTCGTCGGGCTCCTCCTCCCGCTCCGCCTCCTCGGGCTC
CTCCCGCTCGCGCTCGCGCTCCCGCTCCCGCTCCCTCTCCTCCTCCTCGTCCTCGCCCGC
CCGCACCCGGGGCCGCTCCCCTCCCGCCGCCAAGCGCAGTTCACCTGGAGCAAAGAAAGG
GCGATCACCTTCACCCCCTCTCAAAAAAGGGTCACCATCAAGGAAAGGCCGCTCAGCATC
TCCCCCACCGAAGAAAGCTTCACCTCCTAGGAAAGCATCTCCCCCTCCTCAGTCGGTTGT
TCTACACGTTGATCATCTATCCAGAAATGTGAATGAGGCTCATTTGAAGGAGATATTTGG
AAGTTATGGCGAAGTGGTGAATGTGGAGCTATCAATGGACAAATTTGTTAATCTCCCTCG
TGGGTATGGATACATCGAGTTCAAGAAGAGGACTGATGCTGAGAAGGCTCTTCTTTACAT
GGATGGTGTATGCCTTCTGCCCTATGTTTTTTATGTTTATTTTCTTATGCAAATATGACA
AAAAAAATCGCATCTTCTCAGGGGCAAATTGATGGAAATGTTGTCAAGCTGAAGTTCACA
CTGCCACCACGCCAAAAGGCTTCTTCACCTTTAAAGCCACCTCCTCCTCCCCCCAGAAGA
GATGCTCCTCAGAATGATAAAGTTGCTATTGGTGCTGAAAAGGATGCGCAGCAGCGCCCT
GGGGGATCAGCATCTCCACGAAAGAAGCCACCTTCTCCTCCGCGAAAGAGGTCTCCTCCA
AATAGAAGGGCTGAGTCACCCCGGCGTCCACCCAATCCATCTCCAAGGCGTCGTGCTGAT
TCTCCTATTCGTCGTCGACCAGATCTTTCCCCTGTTAGGCGTGGTGACAGAAGACCAGGA
TCTCCAATTAGAAGACGTTCCCCTTCACCTAGAAGGCATAGGTCACCAATGCGGAGGGGT
CGTGGCAGCTTATCACCTCGCAGACGCTCCCCGGGGCCTCCTAGGCGCTCACCTGGGCCT
CCCAGACGGCGCAGGTCACCACCACCAAGGAGATTGAGGAGTCCTCCAAGAAGGCCACCA
CCACCACCTCCCCGTCGTCACAGTCGCTCCCCTCCTCCTCGCCGCCCTCTTCACTCCCGC
TCTAGATCGATTTCTCCTCGCAGCAGGGGGCGAGGACCACCATTGAGGCGTGGAAGGTCG
GATTCATCATATTCTGCATCACCCAGTCCTCCAAGAAAGGGACCAAGAAGGGTGTCAAGG
AGCCGCAGCCCTAGAAGGCCTCCCAGAGGAAGGAGCGGATCTAGCGACAGCGGGAGCAGC
AGCTCTTCCCCAACCCCAAGGCGCAGGTAGAAAGAAAGAAACTCGTAACGTGTGTTGTTC
CTGGCAGGTAAAAAAACTTTCTCTTCTCTCTCGACTGTCACCATGGATTGCGTCTGCATG
CATGTATCTTGCTGTGAGCTCAAGTCAAGAGGCGATCGATGTGAGGGGCGGGACGATGCG
ATGAGGTGCTCGGCATGCCTCCCTGGCATTTGTACTCACAAGACAGACTGTATGATGACG
ACTTGTGTTGATGATTTGCCTGTACTGGAACTATTTTTTTATAATTCTGCGGTTGTTTGT
CAACTACAAATCTGGCTA



Protein Sequence (286 aa)

>BART1_0-u25435.022 286 150831_barley_pseudomolecules
MPSALCFLCLFSYANMTKKIASSQGQIDGNVVKLKFTLPPRQKASSPLKPPPPPPRRDAP
QNDKVAIGAEKDAQQRPGGSASPRKKPPSPPRKRSPPNRRAESPRRPPNPSPRRRADSPI
RRRPDLSPVRRGDRRPGSPIRRRSPSPRRHRSPMRRGRGSLSPRRRSPGPPRRSPGPPRR
RRSPPPRRLRSPPRRPPPPPPRRHSRSPPPRRPLHSRSRSISPRSRGRGPPLRRGRSDSS
YSASPSPPRKGPRRVSRSRSPRRPPRGRSGSSDSGSSSSSPTPRRR