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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAAAAGTCTTGACCGCAATGTTTCTCCTAAATATGAATGGAAGAAATAAAAAAGAGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgcttactactagctcttcacttatatgatttctggatcaactttatacttagaaagtttatagcataaagttcttcattttcttgttgtaca...

Basic information

species Oryza sativa
transcript LOC_Os02g10740.1
intron # 4
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|88526391|gb|CI453125.1|CI453125
EST:     AAAAAAGAGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAG                         TGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCT
genomic: AAAAAAGAGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCT
EST: gi|88553595|gb|CI483717.1|CI483717
EST:     GATCATCCAGCCCCCATGATAAGACACAG                         T-GGCATTCCCGGGATTTAGTTAATTGTTGATTTATGATCTGGTGAAGGCT
genomic: GATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCT
EST: gi|88526015|gb|CI453058.1|CI453058
EST:     TAGTACTCATCAGATCATCAGGCGCCCATGATGAGACACAN                         T-GGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCT-AAGGGC
genomic: TAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAA-GGC
EST: gi|27920867|gb|CB096675.1|CB096675
EST:     AAAAAAGAGTAGTACCCATCAGATCATCAAGCGCCCATGATGAGACACAG                         TGGGCATTCCCGGGATCTAGTTAGTTAGTTGAGTTATGATCTGCTGAAGGC
genomic: AAAAAAGAGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTT-GTTGAGTTATGATCTGCTGAAGGC
EST: gi|88535537|gb|CI464343.1|CI464343
EST:     GTACTCATCAGATCATCAAGCGCCCATGATGAGACACAG                         TGGGCATTCCCGGGATCTAGTTAGTTNTTGAGTTATGATCTGCTGAAGGCT
genomic: GTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCT
EST: gi|88524153|gb|CI452046.1|CI452046
EST:     GAGTAGTACTCATCAGATCATCAAGCNCCCATGATGAGACACAG                         TGGGCATTCCCGGGATGTAGGTAGTTGGTGAGTTATGATCTGCTGAAGGCT
genomic: GAGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCT
EST: gi|88535770|gb|CI465476.1|CI465476
EST:     ACTCATCAGATCATCAAGCGCCCATGATGAGACACAN                         TGGCCATTCCCGGGATCTAGGTTAGTTGTTGANTTATGATCTGCTGAAGGC
genomic: ACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTA-GTTAGTTGTTGAGTTATGATCTGCTGAAGGC
EST: gi|88502675|gb|CI430181.1|CI430181
EST:     AGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAG                         TGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCT
genomic: AGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCT

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: 42 (upstream exon), 34 (downstream exon)
Score: 1

GTTGAAAAGTCTTGACCGCAATGTTTCTCCTAAATATGAATGGAAGAAATAAAAAAGAGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgc ... gtctttgcagTGGGCATTCCCGGGATCTAGTTAGTTGTTGAGTTATGATCTGCTGAAGGCTCCTTTTGCTACTGAATAAGGGGGAAAATTTGTTCATACAAATTGAGATC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAAAAGTCTTGACCGCAATGTTTCTCCTAAATATGAATGGAAGAAATAAAAAAGAGTAGTACTCATCAGATCATCAAGCGCCCATGATGAGACACAGgtatctctgcttactactagctcttcacttatatgatttctggatcaactttatacttagaaagtttatagcataaagttcttcattttcttgttgtaca

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