Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u19417.001

ChromosomeExonStartStopDirection
chr3H1156626357156625511-
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
morexEMB92.531247.725153.7711
morexETI110.211262.922305.133
morexLEA104.45235.415644.554
morexEPI45.902246.954952.0966
morexROO73.393654.747623.428
morexROO2121.895144.416115.801
morexNOD143.83239.228110.437
morexRAC297.784291.344270.117
morexINF169.10487.362274.8317
morexINF276.8393109.0280.8651
morexCAR558.943965.001152.0931
morexCAR157.875618.07617.48639
morexLEM69.513166.577879.7854
morexLOD108.684156.613106.371
morexPAL89.7801101.789101.293
morexSEN38.446338.82439.2674



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os05g14180.1 +2 5e-98 297 169/238 (71%) protein|OsIAA17 - Auxin-responsive Aux/IAA gene family member, expressed
TAIR PP10 AT4G29080 @ ARAPORT
AT4G29080.1 @ TAIR		 +2 2e-58 196 130/270 (48%) Symbols: PAP2, IAA27 | phytochrome-associated protein 2 | chr4:14323665-14325213 REVERSE LENGTH=305
BRACH PP3 Bradi2g07770.1.p +2 2e-129 376 207/228 (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 (1497 bp)

>BART1_0-u19417.001 1497 150831_barley_pseudomolecules
NNNNNNccgCGCGGACGACGACCTGAAAGGCACCGAGCTCCGCCTCGGACTTCCCGGCTG
CGAGTCGCCGGACCGCCGCCCGGTCGCCGCCACCACCACACTGGAGCTTCTGCCCGCCAA
GGGCGCCAAGCGAGGGTTCTCGGACGAGGTCCTGCCGCCTGCGCCGTCTGCCGCCGGCGG
GAAAGGCAAGGAGACGTCCGGGGATGAGAAGGACAAGAAGGTCGCCGCACCGCCGCAGCC
TGCTGCCAAGGCTCAGGTGGTGGGATGGCCACCAATCCGCAGCTACCGCAAGAACACGAT
GGCAACCACCACCAACCAGCTGAAGAGCAGCAAGGAGGATTCTGACGCGAAGCAGGGGCA
AGAGTTTCTGTATGTCAAAGTCAGCATGGATGGCGCGCCTTACCTGAGGAAGGTTGACCT
CAAGACATACAAGAACTATAAGGACCTGTCTCTGGGGCTAGAGAAAATGTTCATTGGCTT
CAGCACCGGTAAAGATGGTGTATCTGAGAACAGAAAGGATGGTGAATACGTGCTGACCTA
CGAAGACAAGGACGGAGACTGGATGCTGGTTGGTGACGTCCCATGGGAGATGTTCACCGA
GTCTTGCCGAAGGCTGAGGGTCATGAAAGGTTCAGATGCAGTTGGACTTGCAGTTCCAAG
GGCAGGGGATAAGTCCAAGAATAAGAACTAAAGCGGTTGCTGCCCACAGTTTGAAGACGG
GGTCGCACATACCGTCTGTACTACCGCATGGTTTTTCTATCCCGCAAGTAAAATCACTCC
GTTACTCTACTGTTGTAAGATTTGTGATGTCTCCTAGAGACTTATGCTTTATATTTTGTC
GTGCCGAAGTTGTTGTACGCATGCTATTTCCATCCGTGTAAATGGTTGGTAAGCAGTGCG
AGAGCTACTGCTGTGATTTGATGACTTCTATGTATTTTGCCAGTGTTGTCCTGAACCGGC
CGTTCGTCGTAAATGTGAGGGTTGCAAGACAATTATTTACCTGATGAACTTTGCTTCCGT
ACACCCTCCTAGAAAAGTTTACAGATTTCGATGTAGGTTAGAAGTTACTGCACTTTAATT
ATTAAATAGAAAAAAGGGCAACATAGTCTTTCGTATCCAAATCAATCTATTCGGTATGTT
TGATCTGCAGGCTAATATGACGACAGTCTTTTTAAGTAAATTTAGGCTGCGTTTGGATTG
AGTGTAAAATAATACAGAGGTATTTTTTTCTACACGTGTAACTTACCGGCCAATGTATAA
TTTCGGGCAGAAAATGAAACGACCGATCGACGCATGCATCTTTTACGGAGGTATTTCCAG
CTGAAACGCTGATCCAAACAGGCCATTAAGATTCATGAAAACTTTTAAGGAGGGTGTACC
GAAGCAAAACTCCTGACTTGTTCAAAAGTTTTTCCCGTTCCATTTATTATACTGTTTGCG
GGTGAGTGGGTTGTTGCTTTGTTCTCCATTTCTTCTGAAACATATGCAATTGCATGG



Protein Sequence (229 aa)

>BART1_0-u19417.001 229 150831_barley_pseudomolecules
XXRADDDLKGTELRLGLPGCESPDRRPVAATTTLELLPAKGAKRGFSDEVLPPAPSAAGG
KGKETSGDEKDKKVAAPPQPAAKAQVVGWPPIRSYRKNTMATTTNQLKSSKEDSDAKQGQ
EFLYVKVSMDGAPYLRKVDLKTYKNYKDLSLGLEKMFIGFSTGKDGVSENRKDGEYVLTY
EDKDGDWMLVGDVPWEMFTESCRRLRVMKGSDAVGLAVPRAGDKSKNKN