Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u35917.008

ChromosomeExonStartStopDirection
chr5H1428281957428281837+
chr5H2428282429428282078+
chr5H3428282701428282511+
chr5H4428283382428283299+
chr5H5428283709428283628+
chr5H6428283908428283785+
chr5H7428284612428284091+


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
morexEMB0.4548080.1718250.370822
morexETI0.5880840.4533490.8785
morexLEA0.581900.4643
morexEPI00.2692740
morexROO1.4284400
morexROO20.308340.5618240
morexNOD00.257740
morexRAC0.3642130.5361250.442395
morexINF10.5123360.5914990.755514
morexINF22.239881.371921.75166
morexCAR50.4977040.490860
morexCAR150.3718740.4631690.323347
morexLEM0.52400601.28526
morexLOD1.347160.2103390.561142
morexPAL0.9169640.8590410.248044
morexSEN0.3030780.4085750.442452



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os09g12800.1 +2 2e-82 264 133/161 (83%) protein|zinc finger Ran-binding domain-containing protein 2, putative, expressed
TAIR PP10 AT1G50300 @ ARAPORT
AT1G50300.1 @ TAIR		 +2 6e-58 196 106/160 (66%) Symbols: TAF15 | TBP-associated factor 15 | chr1:18628818-18631662 REVERSE LENGTH=372
BRACH PP3 Bradi1g19280.1.p +2 6e-105 269 140/160 (88%) 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 (1476 bp)

>BART1_0-u35917.008 1476 150831_barley_pseudomolecules
ACAGATGGCTGGATATATGTCTCGCGGACCCCCAAATGGCTCTATTTATGTATGCAATCT
GCCTCCTGGAACTGATGAGACCATGTTGGCTGAATATTTTGGCACCATAGGGTTGCTAAA
GAAGGACAAAAGGACTGGCCACCCAAAGATTTGGATATACAGGGACAAAGTTACAAATGA
ACCAAAGGGTGATGCAACAGTCACCTATGAAGATCCCCATGCTGCTTCAGCTGCTGTGGA
ATGGTTCAACAATAAGGATTTCCATGGAAGCATCATCCAGGTTCACATAGCTGAGTCAAA
AAACAAAGACACAGTTGATAACTTCACCAATGTGAGCGTCGATGCTGAGATTGTTGGACA
AGATGAATTGGATAACGGGTCAGGCAGGGGTAGAGGACGTGGTGATGGTCCAGCAAAAGC
TTGGCAGCAAGATGGAGATTGGATGTGTCCAAATACAAGGTCTGTTACGATTGCTGTGGC
AATGTAAATTTTGCCTTCCGTGGTGTGTGTAATCGTTGTGGAGCCTCTCGCCCTGCTGGT
GTTAGTGGATCAGGTGGTGGTGGTGGTAGGGGTAGAGGCCGTGGTAGTGATGATGCAAGA
GGCAGTCGTGCTGCTGCTGCTGTTGGTGGTCCTCCTGGGCTGTTTGGTCCTAATGATTGG
CCATGTGTGGCAATGTAAACTGGGCCAAGCGGACCAAATGTAATGTCTGTAACACCTCTA
GGCCAGGTCACAATGAAGGTGGTGTGAGAGGTGGCCGGGGTGGCGGCTTTAAAGAACTTG
ATGAAGAAGAACTAGAAGAAGTACGGAGGCGCCGGAAAGAAGCTGAGGAGGATGATGGAG
AAATGTATGATGAATTTGGTAACCTGAAAAAGAAGTTCCGTGCTAAGTCACATCAAACTG
AGAGTACACCAACTCTTCCTGGGTCTGGACGTGCTGGATGGGAAGTTGAGCACCGTTCCA
CTGAGAGAGAAGGCCGAGAGAGGAGCAGAGATCGGGGCAGGGACGACTACGATGAAAGGG
AAAGCAAGAACAGAGACAGAGGTTCTCATGGAAGAGAGCGGCGCCGTAGCCGAAGCAGGA
GCAGAGACCGCGAGAAGGAGAGGGGGAGGGACAGGGGCAGAGATCGTGGCAACGAGAGAA
GCTGGGAGCGCGGCACTGATCGTGAACGTGATCGCTACAGATGATATGTCAGGAGTTTTG
TCATGTTTGCTTGCCACTTTTCGGTTTTCTGAACCTTTTGTTATGCTGTTGGAGAGCTGT
GGTGTATCACACTGTTATCATTAACATGGGACAAGCTTATTATGTTTGGGTCTAAAGTTC
TCAAAACAGACCGGATCGATGGGTCGTCAGATCATCTGGTACAACGGACCCATCAGATCA
TCTGGTACATCAACGGAATTGCCGAGGAATGACCATCGAGACCTGAAAAAGTCTGGATCA
TAGTATCCTTGCGGCATGAGCAGCATTTGTTCTGAA



Protein Sequence (173 aa)

>BART1_0-u35917.008 173 150831_barley_pseudomolecules
MCGNVNWAKRTKCNVCNTSRPGHNEGGVRGGRGGGFKELDEEELEEVRRRRKEAEEDDGE
MYDEFGNLKKKFRAKSHQTESTPTLPGSGRAGWEVEHRSTEREGRERSRDRGRDDYDERE
SKNRDRGSHGRERRRSRSRSRDREKERGRDRGRDRGNERSWERGTDRERDRYR