Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u35917.006

ChromosomeExonStartStopDirection
chr5H1428280957428280791+
chr5H2428281973428281841+
chr5H3428282429428282078+
chr5H4428282708428282511+
chr5H5428283382428283299+
chr5H6428283709428283628+
chr5H7428283911428283785+
chr5H8428284510428284091+


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
morexEMB0.9711790.7472680.279534
morexETI0.000000006971940.2283680.00679351
morexLEA000
morexEPI2.22951.914970.13846
morexROO0.0000006230821.654321.69548
morexROO22.30750.0000004752260
morexNOD0.8267681.253772.78926
morexRAC0.007358940.00001265160
morexINF15.049112.603541.49931
morexINF215.57119.1973913.2122
morexCAR56.795250.09558263.01769
morexCAR153.429640.0000002592912.71129
morexLEM000.0000000263018
morexLOD00.5931220
morexPAL01.629020.588607
morexSEN1.9664300.655447



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os09g12800.1 +1 1e-100 184 97/125 (78%) protein|zinc finger Ran-binding domain-containing protein 2, putative, expressed
TAIR PP10 AT1G50300 @ ARAPORT
AT1G50300.1 @ TAIR		 +1 1e-63 143 78/125 (62%) Symbols: TAF15 | TBP-associated factor 15 | chr1:18628818-18631662 REVERSE LENGTH=372
BRACH PP3 Bradi1g19280.1.p +1 2e-85 187 102/125 (82%) pacid=32805605 transcript=Bradi1g19280.1 locus=Bradi1g19280 ID=Bradi1g19280.1.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 (1563 bp)

>BART1_0-u35917.006 1563 150831_barley_pseudomolecules
GCCATCCCCAAGCACGCAGTGAGCGCTGAGATCCGCCCAAACCTAGCGCCGTCGCGGCTT
CTCAACCACGCGGCCGCCGCCGCGTTCCCGTCGGCAGAGCACGAGGCGCGCGGTCCTCCG
CGCACGCCTTCGATCCGCGCCGTCAACCTCGGCGCATCCCGGACTAGATGGCTGGATATA
TGTCTCGCGGACCCCCAAATGGCTCTATTTATGTATGCAATCTGCCTCCTGGAACTGATG
AGACCATGTTGGCTGAATATTTTGGCACCATAGGGTTGCTAAAGGTATGGGTCTTACCAG
AAGGACAAAAGGACTGGCCACCCAAAGATTTGGATATACAGGGACAAAGTTACAAATGAA
CCAAAGGGTGATGCAACAGTCACCTATGAAGATCCCCATGCTGCTTCAGCTGCTGTGGAA
TGGTTCAACAATAAGGATTTCCATGGAAGCATCATCCAGGTTCACATAGCTGAGTCAAAA
AACAAAGACACAGTTGATAACTTCACCAATGTGAGCGTCGATGCTGAGATTGTTGGACAA
GATGAATTGGATAACGGGTCAGGCAGGGGTAGAGGACGTGGTGATGGTCCAGCAAAAGCT
TGGCAGCAAGATGGAGATTGGATGTGTCCAAATACAAGGTCTGTTACGATTGCTGTGGCA
ATGTAAATTTTGCCTTCCGTGGTGTGTGTAATCGTTGTGGAGCCTCTCGCCCTGCTGGTG
TTAGTGGATCAGGTGGTGGTGGTGGTAGGGGTAGAGGCCGTGGTAGTGATGATGCAAGAG
GCAGTCGTGCTGCTGCTGCTGTTGGTGGTCCTCCTGGGCTGTTTGGTCCTAATGATTGGC
CATGTACGATGTGTGGCAATGTAAACTGGGCCAAGCGGACCAAATGTAATGTCTGTAACA
CCTCTAGGCCAGGTCACAATGAAGGTGGTGTGAGAGGTGGCCGGGGTGGCGGCTTTAAAG
AACTTGATGAAGAAGAACTAGAAGAAGTACGGAGGCGCCGGAAAGAAGCTGAGGAGGATG
ATGGAGAAATGTATGATGAATTTGGTAACCTGAAAAAGAAGTTCCGTGCTAAGTCACATC
AAACTGAGAGTACACCAACTCTTCCTGGGTCTGGACGTGCTGGATGGGAAGTTGAGCACC
GTGGTTCCACTGAGAGAGAAGGCCGAGAGAGGAGCAGAGATCGGGGCAGGGACGACTACG
ATGAAAGGGAAAGCAAGAACAGAGACAGAGGTTCTCATGGAAGAGAGCGGCGCCGTAGCC
GAAGCAGGAGCAGAGACCGCGAGAAGGAGAGGGGGAGGGACAGGGGCAGAGATCGTGGCA
ACGAGAGAAGCTGGGAGCGCGGCACTGATCGTGAACGTGATCGCTACAGATGATATGTCA
GGAGTTTTGTCATGTTTGCTTGCCACTTTTCGGTTTTCTGAACCTTTTGTTATGCTGTTG
GAGAGCTGTGGTGTATCACACTGTTATCATTAACATGGGACAAGCTTATTATGTTTGGGT
CTAAAGTTCTCAAAACAGACCGGATCGATGGGTCGTCAGATCATCTGGTACAACGGACCC
ATC



Protein Sequence (174 aa)

>BART1_0-u35917.006 174 150831_barley_pseudomolecules
MCGNVNWAKRTKCNVCNTSRPGHNEGGVRGGRGGGFKELDEEELEEVRRRRKEAEEDDGE
MYDEFGNLKKKFRAKSHQTESTPTLPGSGRAGWEVEHRGSTEREGRERSRDRGRDDYDER
ESKNRDRGSHGRERRRSRSRSRDREKERGRDRGRDRGNERSWERGTDRERDRYR