Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u35721.006

ChromosomeExonStartStopDirection
chr5H1405760204405760074+
chr5H2405760512405760450+
chr5H3405761523405761364+
chr5H4405762633405762486+
chr5H5405762807405762730+
chr5H6405763442405763358+
chr5H7405763590405763535+
chr5H8405766075405765455+


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
morexEMB169.677198.973202.508
morexETI13.360816.681114.637
morexLEA84.765148.335139.4258
morexEPI4.3386913.88047.94598
morexROO73.753392.189352.8816
morexROO259.00456.493152.813
morexNOD331.55394.881627.8066
morexRAC66.767172.290574.1004
morexINF191.083596.264576.755
morexINF252.947965.078561.9602
morexCAR5131.952137.076137.872
morexCAR1516.223617.171315.4344
morexLEM28.971920.552330.3528
morexLOD74.415157.480891.0247
morexPAL60.220360.300468.0103
morexSEN11.780219.891320.7291



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os02g21250.2 +3 2e-99 295 170/182 (93%) protein|clathrin adaptor complex small chain domain containing protein, expressed
TAIR PP10 AT3G09800 @ ARAPORT
AT3G09800.1 @ TAIR		 +3 2e-72 226 127/178 (71%) Symbols: | SNARE-like superfamily protein | chr3:3006731-3007916 REVERSE LENGTH=179
BRACH PP3 Bradi4g08770.4.p +3 6e-104 307 177/182 (97%) pacid=32783612 transcript=Bradi4g08770.4 locus=Bradi4g08770 ID=Bradi4g08770.4.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 (1342 bp)

>BART1_0-u35721.006 1342 150831_barley_pseudomolecules
CCAGCTCGTCCATTTCCGCTCGCCTAATCCCTCCCGTCTTTCTCTACACTCGTCTGCTGC
ATCTCAGATCTCGCGGGCACCAACAAACCAAAGCAAAGCTCTCCCGCTGTCCCGATCACT
CTCCCTTCCAGGAAGCTTGGACCGGAGGAAGGTGCTGAGAGGGCGGAAAGGAGGCCATGG
GGGAATTCTCCAAGGAATCTTGCCCGTCTGTGAAGAACATTTTGCTACTGGATTCTGAGG
GAAAGCGCGTTGCTGTGAAGTACTTCTCGGATGATTGGCCGAACAACGCATCTAGGTTGA
CCTTTGAAAAGTCCATTTTTACTAAAACTCTGAAGACAAATGCACGCTCAGAAGCTGAGA
TAACATTGCTTGATGGTAATATTGTTGTTTACAAGTTTGTACAAGACCTTCACTTCTTCG
TCACTGCCGGAGATGATGAGAATGAGCTAATCATAGCAAATGTGCTACAGGGTTTTGCTG
ATTCGGTTGGTCTTCTACTCAGGGGTGACGTTGAGAAGAGGACTGCACTTGAGAACTTGG
ACTTGATACTTCTCTGCATTGATGAGATTATTGATGGCGGCATAATTCTTGAAACAGATG
CGAATACCATTGCGGGGAAGGTTGCAACCAATGCTGCTGACGGTTCTGTTCCCTTCTCTG
AGCAGACAATATCCCAAGCTCTGGCCACAGCCAGGGAACACTTTGCAAGATCTCTTCTGA
AGTTTACCCTACCAAACGAATTTCAAATGCCACAAAACTTTAATATGATTTTTTCTGGAC
TATATGAAGACCTGCAAGCATCAGAAGTGGACGAGAGGCCGAACGAGGTAGGCACAAGCC
AACAGGGCGCGGCCGCGCCCTAATGACTTGTGCCCCCCTAGATGCCTCCCGCCGTCCCTC
TCTGACCTATAAATTCACAAATATTCCGATGCACTCCCGAAACACTTTTTCCGCCGCCGC
AAGTCTCTGTTCTGACGGAAGGCCATCTAAACCTCCATTCCGGCGATCTGTCGGAGGGGA
GATCAGTCACGGAGGGCCTCTACATCAACCTTGTTGCCCTCACCGTGATGTGTGAGTAGT
TTACCACATACCTACGGGTCCGTAGGCAGTACCTAGATGACAATCTCTCTCTCTTATGAT
CTTCAATACCATGTTCATCGCATCTTCGCTTTGATCTATCCGATGTAATCACTATGTATG
GTGTGTTTGTTGGGGTCCGATGAATTGTGGGTTTATGTTCAGATTATTCATGAAAAGTAT
TTGAGTCATCTCTGATTATTATGATTCTTAATTGCATGATCATCATAGCTTCATAATGCT
CTTCGATCTATTGAGATAGTTT



Protein Sequence (228 aa)

>BART1_0-u35721.006 228 150831_barley_pseudomolecules
MGEFSKESCPSVKNILLLDSEGKRVAVKYFSDDWPNNASRLTFEKSIFTKTLKTNARSEA
EITLLDGNIVVYKFVQDLHFFVTAGDDENELIIANVLQGFADSVGLLLRGDVEKRTALEN
LDLILLCIDEIIDGGIILETDANTIAGKVATNAADGSVPFSEQTISQALATAREHFARSL
LKFTLPNEFQMPQNFNMIFSGLYEDLQASEVDERPNEVGTSQQGAAAP