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

CGGCTCAACCGGGAGGCCCGGAAGAAGCCGCTGCCGCTCGGCTGCCACGACATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcctctccctccagcgaatttccagttttaatacgaaacagtactgagctaacatctgatggtacataaaaggctaatcggagttgagatcgtg...

Basic information

species Oryza sativa
transcript LOC_Os01g43710.1
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|58587978|gb|CF986286.1|CF986286
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|58688086|gb|CK076773.1|CK076773
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|29620925|gb|CB625936.1|CB625936
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|29620835|gb|CB625846.1|CB625846
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|66919240|gb|CX106088.1|CX106088
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGACCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|29620809|gb|CB625820.1|CB625820
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|66918138|gb|CX104986.1|CX104986
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|29620813|gb|CB625824.1|CB625824
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|426509|gb|D22332.1|D22332
EST:     GTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: GTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|58688272|gb|CK076959.1|CK076959
EST:     TGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: TGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|29620837|gb|CB625848.1|CB625848
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|29620874|gb|CB625885.1|CB625885
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|33799605|gb|CF325663.1|CF325663
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|58585667|gb|CF983975.1|CF983975
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
EST: gi|66918216|gb|CX105064.1|CX105064
EST:     CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACG                         GGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG
genomic: CATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAG

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: 72 (upstream exon), 59 (downstream exon)
Score: 52

CGGCTCAACCGGGAGGCCCGGAAGAAGCCGCTGCCGCTCGGCTGCCACGACATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcct ... gtaactgcagGGAAACCATCATTCACTTGGTTTGGCCCAACGCCAAGAGTGATGATTTCAGACCCTGAATCAATAAGGGAAGTTATGTCTAATAAGTTTGGCCACTATGG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGCTCAACCGGGAGGCCCGGAAGAAGCCGCTGCCGCTCGGCTGCCACGACATCATCCCGCGCGTGCTGCCGATGTTCAGCAAAGCCGTTGAGGAGCACGgtatagtcctctccctccagcgaatttccagttttaatacgaaacagtactgagctaacatctgatggtacataaaaggctaatcggagttgagatcgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctc