Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u19417.003

ChromosomeExonStartStopDirection
chr3H1156626354156625511-
chr3H2156627286156627225-
chr3H3156628029156627930-
chr3H4156628966156628728-
chr3H5156629835156629587-


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
morexEMB33.048831.370340.5542
morexETI56.4725156.505161.91
morexLEA75.993518.123616.3434
morexEPI22.779220.597522.6252
morexROO35.108721.037210.4077
morexROO242.21743.433736.3526
morexNOD84.435862.741475.5785
morexRAC94.9371105.17129.257
morexINF143.818446.751949.3969
morexINF260.30970.077871.254
morexCAR541.16944.398847.1626
morexCAR155.127492.750686.7352
morexLEM26.299424.288628.6159
morexLOD48.844537.686733.3787
morexPAL33.185939.684733.8233
morexSEN17.489413.257612.4422



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os05g14180.1 +2 3e-99 300 168/237 (71%) protein|OsIAA17 - Auxin-responsive Aux/IAA gene family member, expressed
TAIR PP10 AT4G29080 @ ARAPORT
AT4G29080.1 @ TAIR		 +2 1e-59 198 129/269 (48%) Symbols: PAP2, IAA27 | phytochrome-associated protein 2 | chr4:14323665-14325213 REVERSE LENGTH=305
BRACH PP3 Bradi2g07770.1.p +2 2e-130 379 206/227 (91%) pacid=32771633 transcript=Bradi2g07770.1 locus=Bradi2g07770 ID=Bradi2g07770.1.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 (1494 bp)

>BART1_0-u19417.003 1494 150831_barley_pseudomolecules
NNNNNNccgCGCGGACGACGACCTGAAAGGCACCGAGCTCCGCCTCGGACTTCCCGGCTG
CGAGTCGCCGGACCGCCGCCCGGTCGCCGCCACCACCACACTGGAGCTTCTGCCCGCCAA
GGGCGCCAAGCGAGGGTTCTCGGACGAGGTCCTGCCGCCTGCGCCGTCTGCCGCCGGCGG
GAAAGGCAAGGAGACGTCCGGGGATGAGAAGGACAAGAAGGTCGCCGCACCGCCGCAGCC
TGCTGCCAAGGCTCAGGTGGTGGGATGGCCACCAATCCGCAGCTACCGCAAGAACACGAT
GGCAACCACCACCAACCAGCTGAAGAGCAGCAAGGAGGATTCTGACGCGAAGCAGGGGCA
AGAGTTTCTGTATGTCAAAGTCAGCATGGATGGCGCGCCTTACCTGAGGAAGGTTGACCT
CAAGACATACAAGAACTATAAGGACCTGTCTCTGGGGCTAGAGAAAATGTTCATTGGCTT
CAGCACCGGTAAAGATGGTGTATCTGAGAACAGAAAGGATGGTGAATACGTGCTGACCTA
CGAAGACAAGGACGGAGACTGGATGCTGGTTGGTGACGTCCCATGGGAGATGTTCACCGA
GTCTTGCCGAAGGCTGAGGGTCATGAAAGGTTCAGATGCAGTTGGACTTGTTCCAAGGGC
AGGGGATAAGTCCAAGAATAAGAACTAAAGCGGTTGCTGCCCACAGTTTGAAGACGGGGT
CGCACATACCGTCTGTACTACCGCATGGTTTTTCTATCCCGCAAGTAAAATCACTCCGTT
ACTCTACTGTTGTAAGATTTGTGATGTCTCCTAGAGACTTATGCTTTATATTTTGTCGTG
CCGAAGTTGTTGTACGCATGCTATTTCCATCCGTGTAAATGGTTGGTAAGCAGTGCGAGA
GCTACTGCTGTGATTTGATGACTTCTATGTATTTTGCCAGTGTTGTCCTGAACCGGCCGT
TCGTCGTAAATGTGAGGGTTGCAAGACAATTATTTACCTGATGAACTTTGCTTCCGTACA
CCCTCCTAGAAAAGTTTACAGATTTCGATGTAGGTTAGAAGTTACTGCACTTTAATTATT
AAATAGAAAAAAGGGCAACATAGTCTTTCGTATCCAAATCAATCTATTCGGTATGTTTGA
TCTGCAGGCTAATATGACGACAGTCTTTTTAAGTAAATTTAGGCTGCGTTTGGATTGAGT
GTAAAATAATACAGAGGTATTTTTTTCTACACGTGTAACTTACCGGCCAATGTATAATTT
CGGGCAGAAAATGAAACGACCGATCGACGCATGCATCTTTTACGGAGGTATTTCCAGCTG
AAACGCTGATCCAAACAGGCCATTAAGATTCATGAAAACTTTTAAGGAGGGTGTACCGAA
GCAAAACTCCTGACTTGTTCAAAAGTTTTTCCCGTTCCATTTATTATACTGTTTGCGGGT
GAGTGGGTTGTTGCTTTGTTCTCCATTTCTTCTGAAACATATGCAATTGCATGG



Protein Sequence (228 aa)

>BART1_0-u19417.003 228 150831_barley_pseudomolecules
XXRADDDLKGTELRLGLPGCESPDRRPVAATTTLELLPAKGAKRGFSDEVLPPAPSAAGG
KGKETSGDEKDKKVAAPPQPAAKAQVVGWPPIRSYRKNTMATTTNQLKSSKEDSDAKQGQ
EFLYVKVSMDGAPYLRKVDLKTYKNYKDLSLGLEKMFIGFSTGKDGVSENRKDGEYVLTY
EDKDGDWMLVGDVPWEMFTESCRRLRVMKGSDAVGLVPRAGDKSKNKN