Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgctttgtggttaatacattatatactgtacatgtttggttgataatagtcgaatctaatctgcggtaattctttattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCACAAAGGATTCCTATGACGCACGGAGATTGGCAATGAACTCAGGGTATCC

Basic information

species Oryza sativa
transcript LOC_Os01g43910.1
intron # 9
splice site 3'
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|66923351|gb|CX110199.1|CX110199
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|58681598|gb|CK070285.1|CK070285
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|42793952|gb|AB117851.1|AB117851
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|44679557|gb|CR292991.1|CR292991
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGGGTGACAACAG                         CAAGACCAGGAAGAGTTGTAGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|58675747|gb|CK064434.1|CK064434
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|33690146|gb|CF318385.1|CF318385
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|88359064|gb|CI679580.1|CI679580
EST:     AAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: AAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|88588243|gb|CI706047.1|CI706047
EST:     AAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: AAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|88458211|gb|CI695391.1|CI695391
EST:     AAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: AAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|58672466|gb|CK061152.1|CK061152
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
EST: gi|88392367|gb|CI612841.1|CI612841
EST:     TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAG                         CAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA
genomic: TTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCA

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: 75 (upstream exon), 71 (downstream exon)
Score: 36

GATAAACCATCTGATGAACCCTATAGCAATCCCCGGGAATTTGACAGATTTTCTGGCAATGCCCCGAGGACCTCACAAGCTCCACAAAGAGTGCCAACAGgtgctttgtg ... tattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCACAAAGGATTCCTATGACGCACGGAGATTGGCAATGAACTCAGGGTATCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acatgtttggttgataatagtcgaatctaatctgcggtaattctttattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCACAAAGGATTCCTATGACGCACGGAGATTGGCAATGAACTCAGGGTATCC
                        atctaat  putative branch site (score: 36)
                                        ttctttatttt  putative PPT
                                     taattctttattttac  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgctttgtggttaatacattatatactgtacatgtttggttgataatagtcgaatctaatctgcggtaattctttattttacagCAAGACCAGGAAGAGTTGTTGGTCCAGTATTGCCTTATGAAAATGGTGCCACAAAGGATTCCTATGACGCACGGAGATTGGCAATGAACTCAGGGTATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT