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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatctgatgcacatccaagatttattcaattattagctgatggttttgccgaaacttgtgctgtttatgcttgttttcttgtatcctaatggttaatgtttacctattctttctgtag

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 14
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|29668943|gb|CB665218.1|CB665218
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|218502213|gb|FG961004.1|FG961004
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTGAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|29640538|gb|CB645547.1|CB645547
EST:     GTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: GTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|218490049|gb|FG963619.1|FG963619
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|29642463|gb|CB647470.1|CB647470
EST:     GAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: GAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|218479902|gb|FG948663.1|FG948663
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|33676232|gb|CF304471.1|CF304471
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCT
EST: gi|29642462|gb|CB647469.1|CB647469
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAAACTACTGTGCTGA
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGA
EST: gi|218493259|gb|FG949070.1|FG949070
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|33676868|gb|CF305107.1|CF305107
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAAC-TCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|58671293|gb|CK059979.1|CK059979
EST:     TGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGAGTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: TGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|29663066|gb|CB659341.1|CB659341
EST:     TTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|58673473|gb|CK062159.1|CK062159
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|58670000|gb|CK058686.1|CK058686
EST:     CTTGGGCACGTGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGT
EST: gi|58681408|gb|CK070095.1|CK070095
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|58585822|gb|CF984130.1|CF984130
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|29626361|gb|CB631372.1|CB631372
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|58607251|gb|CK035284.1|CK035284
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|218502862|gb|FG946696.1|FG946696
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|218499296|gb|FG965743.1|FG965743
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCAATCAAAC-TACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCA-TCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTT
EST: gi|218497744|gb|FG966597.1|FG966597
EST:     CACATGAGCATGAACCTGTAACGACACTGTTA-ATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|33676662|gb|CF304901.1|CF304901
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
EST: gi|8956808|gb|BE230611.1|BE230611
EST:     CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAG                         TCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT
genomic: CTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 62 (upstream exon), 73 (downstream exon)
Score: 49

GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatct ... ctttctgtagTCCATCAAACCTACTGTGCTGATTGGAACATCCGGAGTTGGCAAAACTTTTACTAAAGAAGTTATTGAGGCCATGGCTTCCTTTAACGAG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGTTGATCGTTAACTCACGAAAAGAATCCCTCCAGGCATTTAAAAAGCCTTGGGCACATGAGCATGAACCTGTAACGACACTGTTAGATGCTGTCCAGgtattcatctgatgcacatccaagatttattcaattattagctgatggttttgccgaaacttgtgctgtttatgcttgttttcttgtatcctaatggttaatgtttacctattctttctgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG