Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGCGACCATTATGGGTCCTCCAGATAGTCCCTATGCTGGTGGAGTTTTCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagttagtcttattctggggcaaacttttcctatatttgctacttttattgaagatgaaccctctctccgtctcatggattctcactactacttc...

Basic information

species Oryza sativa
transcript LOC_Os01g60410.2
intron # 3
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|58593001|gb|CF991309.1|CF991309
EST:     CTTAGTGAATATTCAGTTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: CTTAGTGAATATTCA-TTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|1631641|gb|C19370.1|C19370
EST:     TCTNAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTNAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88836129|gb|CI371234.1|CI371234
EST:     CGTAGTTGAATATTCATTTCCCCCCGGAGTACCCCTTCAAGCCTCCAAA-                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: CTTAG-TGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58684372|gb|CK073059.1|CK073059
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTAAAGCCTCCAAAG                         GTATCTTTTAAGACAACGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88511626|gb|CI439132.1|CI439132
EST:     TGTTAGTGGATATTCATTTCCCCCCGGAGTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88982118|gb|CI027695.1|CI027695
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58683224|gb|CK071911.1|CK071911
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|112785779|gb|EE591396.1|EE591396
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88981515|gb|CI027133.1|CI027133
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|163917796|gb|EG712134.1|EG712134
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|33810775|gb|CF331282.1|CF331282
EST:     ACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: ACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88979909|gb|CI026203.1|CI026203
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58683175|gb|CK071862.1|CK071862
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|38470328|gb|CF954459.1|CF954459
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58594364|gb|CF992672.1|CF992672
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88391945|gb|CI683764.1|CI683764
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88588887|gb|CI706732.1|CI706732
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58677585|gb|CK066272.1|CK066272
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|33692170|gb|CF320409.1|CF320409
EST:     AGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: AGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58600178|gb|CK010706.1|CK010706
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|33688145|gb|CF316384.1|CF316384
EST:     TCTTAGTGAATATTCATTTCCCCCCGGAATACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88511520|gb|CI439026.1|CI439026
EST:     CTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: CTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58592288|gb|CF990596.1|CF990596
EST:     TCTTAGTGAATATGCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|218501187|gb|FG953295.1|FG953295
EST:     CTTAGTGAATATTCATTTCCCCCCGGNACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: CTTAGTGAATATTCATTTCCCCCCGG-ACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|33688146|gb|CF316385.1|CF316385
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88962910|gb|CI025396.1|CI025396
EST:     TTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAGACATCAATAGCAATGGAAGC
genomic: TTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|87006558|gb|CI294941.1|CI294941
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58690981|gb|CK079668.1|CK079668
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|33810778|gb|CF331283.1|CF331283
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58592931|gb|CF991239.1|CF991239
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|396941307|gb|HO188516.1|HO188516
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58601287|gb|CK011815.1|CK011815
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|88222470|gb|CI222426.1|CI222426
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|3107124|gb|D42862.1|D42862
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58600789|gb|CK011317.1|CK011317
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCCATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|15847912|gb|BI796188.1|BI796188
EST:     CCCTTCAAGCCTCCAAA-                         GTATCTTTTAAGACAAAGGTCTTCCATCC-AACATCGAATAGCAATGGAAG
genomic: CCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATC-AATAGCAATGGAAG
EST: gi|163925769|gb|EG714605.1|EG714605
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|58595019|gb|CF993327.1|CF993327
EST:     TCTGAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTTAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
EST: gi|86256681|gb|CI061444.1|CI061444
EST:     TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAG                         GTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC
genomic: TCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagtt ... tttttttcagGTATCTTTCAAGACAAAGGTCTTCCATCCAAACATCAATAGCAATGGAAGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGCGACCATTATGGGTCCTCCAGATAGTCCCTATGCTGGTGGAGTTTTCTTAGTGAATATTCATTTCCCCCCGGACTACCCCTTCAAGCCTCCAAAGgttagcagttagtcttattctggggcaaacttttcctatatttgctacttttattgaagatgaaccctctctccgtctcatggattctcactactacttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ccctctc