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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGCAACCTCGCGCCGACCATCGCGCCGCCGCTGCTCGTGCTCACCGTGCAGCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacgcggatccctttttcctcctctttcaccggattgatccctttttccccttcttgaatccgttgttgattttgggattgtgtgcttcttctgctccgcgtgtgtgatag

Basic information

species Oryza sativa
transcript LOC_Os01g32780.1
intron # 1
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|86854099|gb|CI252090.1|CI252090
EST:     CCGCT-CTTCCCCTGCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: CCGCTCCTCCCCCT-CGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|86531544|gb|CI171750.1|CI171750
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88590700|gb|CI707581.1|CI707581
EST:     CCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCCTCCCCTC                         TGGGCACCCCCGTTGTA
genomic: CCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGC-TCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTA
EST: gi|88365333|gb|CI679967.1|CI679967
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88352879|gb|CI678908.1|CI678908
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88451899|gb|CI694675.1|CI694675
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88573177|gb|CI664748.1|CI664748
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|58594365|gb|CF992673.1|CF992673
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88352703|gb|CI678724.1|CI678724
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|58591025|gb|CF989333.1|CF989333
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88590296|gb|CI709139.1|CI709139
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGA
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGA
EST: gi|88458290|gb|CI695673.1|CI695673
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCC
EST: gi|88444936|gb|CI696378.1|CI696378
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|86253249|gb|CI058174.1|CI058174
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|55415560|gb|CV727936.1|CV727936
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88434747|gb|CI691036.1|CI691036
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|218502682|gb|FG963566.1|FG963566
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88325391|gb|CI675189.1|CI675189
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88588503|gb|CI706324.1|CI706324
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|218488077|gb|FG946106.1|FG946106
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|218499937|gb|FG948455.1|FG948455
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88377819|gb|CI637953.1|CI637953
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|10930789|gb|AU161063.1|AU161063
EST:     TCCGCCGCCTCCTTCGGCTCCCCCTN                         TGGGCACCCCCGTTGTAGCCCCGGAGCTTGATCAAGNCGATGCAGGAGCA
genomic: TCCGCCGCCTCCTTCGGCT-CCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGC-TGATCAAGGCGATGCAGGAGCA
EST: gi|58585588|gb|CF983896.1|CF983896
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88429234|gb|CI690128.1|CI690128
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAG
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAG
EST: gi|88584114|gb|CI701644.1|CI701644
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88587488|gb|CI705238.1|CI705238
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88581302|gb|CI698279.1|CI698279
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|218494638|gb|FG968655.1|FG968655
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTAGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGC
EST: gi|88352849|gb|CI678876.1|CI678876
EST:     GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTC                         TGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAG
genomic: GCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAG

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: 73 (upstream exon), 75 (downstream exon)
Score: 35

CGCAACCTCGCGCCGACCATCGCGCCGCCGCTGCTCGTGCTCACCGTGCAGCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacg ... tgtgtgatagTGGGCACCCCCGTTGTAGCCCCGGAGCTGATCAAGGCGATGCAGGAGCAGCAGCAGCAGCTCTCGCAGGCGCTCCTCGACAAGGCCAAGCAGATCTGCGC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGCAACCTCGCGCCGACCATCGCGCCGCCGCTGCTCGTGCTCACCGTGCAGCCGCTCCTCCCCCTCGGCTACGTCTCCGCCGCCTCCTTCGGCTCCCCTCgtacgtgacgcggatccctttttcctcctctttcaccggattgatccctttttccccttcttgaatccgttgttgattttgggattgtgtgcttcttctgctccgcgtgtgtgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC