Transcript Data
Barley RTD
Links



Exon Structure of BART1_0-u24401.012

ChromosomeExonStartStopDirection
chr3H1659169943659169818+
chr3H2659170834659170760+
chr3H3659171437659171284+
chr3H4659171629659171536+
chr3H5659172666659172481+
chr3H6659172823659172776+
chr3H7659173083659172898+
chr3H8659173257659173171+
chr3H9659173653659173567+
chr3H10659174501659173736+


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
morexEMB000
morexETI000
morexLEA000.116169
morexEPI00.7734610
morexROO000
morexROO2000
morexNOD000
morexRAC000
morexINF10.28420800
morexINF2000.729935
morexCAR500.5507420
morexCAR15000.705607
morexLEM000.458161
morexLOD0.7761700
morexPAL000
morexSEN000



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

DatabaseHitFrameE-valueScore% IdentityDescription
Rice PP7 LOC_Os01g70920.2 +3 1e-136 401 207/301 (69%) protein|cullin-1, putative, expressed
TAIR PP10 AT4G02570 @ ARAPORT
AT4G02570.4 @ TAIR		 +3 1e-35 142 105/319 (33%) Symbols: CUL1 | cullin 1 | chr4:1129315-1133435 FORWARD LENGTH=738
BRACH PP3 Bradi2g60057.3.p +3 3e-160 461 236/304 (78%) pacid=32775524 transcript=Bradi2g60057.3 locus=Bradi2g60057 ID=Bradi2g60057.3.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 (1809 bp)

>BART1_0-u24401.012 1809 150831_barley_pseudomolecules
AAACCCCTCGAAAAAGCTGAAACCCGTCCCCCAATCCGCCGTCGGCTGCCCTCCTCACCC
CTACCGCGAACGGCAGGCGAGACGGCGGCGGCGGCGAGCACCGCCCGATCCTCTCCCCCC
TCGTCGGCTTTCTATTGAAAACTGAGTATTGCTCAGTTGGTGGGGGCGCTCGAGCATCAC
CCCGCCAAACTGCCCACCAAGTTCACTGTAGGAGCAAAGCAGTAAAAATGAATGCGCACC
TCAGCTTTGAGGATGGCTGGAAGGTCCTGGAACAGGGCATTTTGACATGCTCAAAGATTT
TGGAGGGTTCCACTGGTACAAGGCCTACTGTTGCTGAGTACATGAATTGCTATGACTGTG
CTTATAGAATGGCTGTGCAGACAACCAGCTATTGTGAAGAGATGTACAATGGTTACAGGA
CTACACTTGCAGAATCTGTTCGTGCACTGGTTTTACCCCATCTGATGCACAAGAGAGATG
ACTACCTTTTGAGACAGCTTGAGAAAATGTGGTCGAACTATTGTATCATGGTTAAATGTA
TATCTGGCTTCTTCAACTATTTGGACCGTTGCTTTGTTGAGCAAAGAAAGCTACCTTGTC
TTGAAGACACTGCTGCCACTTCTTTTTTCTCGACAGTCTTTTCGTTCTTTAGCCATGAAG
TATCAGAGGCTCTACTGACTTTGATTCGCCAAGAGCGTGATGGAAGCAATGTTGATATGG
ACATCTTGATGGTCATTATGCGTGGCATATGTCGCTCTGAAGTCAAATCCTTCATGAGAA
ATGCTGTTGTCCAAGATACATATGCTTACTACTCCAGGAAAAGTTCTGAATGGATAGTTC
AGTACCCTCTACAAGATTACCTTGCCATGGTCCAGGATTGTATGGAGAAGGAAACCATGA
GATTGATGAGCTATCTGCATATTCCTGAGGGAGATAGCACAGAACTCTGTTTGAAGGTTG
TTAGTGCTCCATTGATGCAAATGTATGACAGCTATGCAAGAGAGAAACAGATTGGTGGCC
AACTTTTGCTTCAAACATACAAGACTGTGGAGGATGATCTGCTGGCCAGATGCAATCGCT
TGACAATTGACAGCGGCGTGGACAACAGTTCTGGCAGTTACATGGAGTAGAAAGGAAATG
CACTTCAGCTAACATTCATCTATAACCAAGATTACATACAGGAAGGGGTTCTAGAACATG
GCCTACATCTGGGGGAATTTTTTGTGCGGCTGCTCGGTTTTTGGTACCGTGGATTTTGTT
GGCAAGGTTCGCCTAGATTAAACGCTGTACTGAATGCGAAGGGGATACCTCTTAAGTGCT
GCCTCCTACCCCATTATGGTCAACAGCATCTGAAATGTACAGGATGGCTGGTCAATTTAT
GCCAATGGCAGTTTATTTTGATCGTTGTCTAGCGAACATTAGGCCGGTCAGCACCTAGCA
CTCTTAGTGGCTGGACATGGAGTATGTGGTCATGACACCAGAATGATCGGTGCATTGCCT
GTGTGCCTTTTGCTTGCGAGCTTCTGATGCTGTCTATGGTCTAAGCTTATCTATGACTTG
ATGTTACTTTCCTGTGTTTGTGTGCTTGCCTAAATTGCTAAACTGTAGGTTGGATGTGTT
TTCGCTTATTTCATGTCAAGTTTGCTGTTATGGTTGCAGTTCTTTCCTTGGTGGGCCATA
ATTGTTTGCAATTTTAGATTAGATTATAAACCCTGGTTCCATTATTAATGGGGCATGGAT
CTTATACCTTGTTGGTCTGACTTTAAGCTATTCTTGCGGCATATCCATTTTCTTGAATTA
ATAAAGTGC



Protein Sequence (300 aa)

>BART1_0-u24401.012 300 150831_barley_pseudomolecules
MNAHLSFEDGWKVLEQGILTCSKILEGSTGTRPTVAEYMNCYDCAYRMAVQTTSYCEEMY
NGYRTTLAESVRALVLPHLMHKRDDYLLRQLEKMWSNYCIMVKCISGFFNYLDRCFVEQR
KLPCLEDTAATSFFSTVFSFFSHEVSEALLTLIRQERDGSNVDMDILMVIMRGICRSEVK
SFMRNAVVQDTYAYYSRKSSEWIVQYPLQDYLAMVQDCMEKETMRLMSYLHIPEGDSTEL
CLKVVSAPLMQMYDSYAREKQIGGQLLLQTYKTVEDDLLARCNRLTIDSGVDNSSGSYME