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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGTACGGTGAAGATGCTCTCAAGGAGGGGATGGGTCCTGGTGGTGGGATGCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagacatgagaagcagctcaattcaacctcctggtgattgtggtttgcttagattttgactggctctcattgtggtctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g57340.1
intron # 2
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|58686504|gb|CK075191.1|CK075191
EST:     GCATGACCCATTTGACATCTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTA-GGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|44677099|gb|CR290533.1|CR290533
EST:     TTTCCTCATCCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: TTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|38472777|gb|CF956909.1|CF956909
EST:     GCATGACCCATTTGACATCTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|29680484|gb|CB676759.1|CB676759
EST:     GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|2311036|gb|C27191.1|C27191
EST:     ATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: ATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|218502146|gb|FG950394.1|FG950394
EST:     GCATGACCCATTTGACATCTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|58658806|gb|CK047486.1|CK047486
EST:     GCATGACCCATTTGACATCTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|218499104|gb|FG960771.1|FG960771
EST:     GCATGACCCATTTGACATCTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|13420510|gb|AU174600.1|AU174600
EST:     GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|218495063|gb|FG965805.1|FG965805
EST:     GCATGACCCATTTGACATCTTTTCTTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC
EST: gi|88382753|gb|CI682644.1|CI682644
EST:     GCATGACCCATTTGACATTTCTTCCTCATTCTTCGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTG
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTG
EST: gi|9865401|gb|AU101151.1|AU101151
EST:     GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAG                         GTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTNGTTCACC
genomic: GCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACC

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), 71 (downstream exon)
Score: 147

CAGTACGGTGAAGATGCTCTCAAGGAGGGGATGGGTCCTGGTGGTGGGATGCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagaca ... tggtctgcagGTGGTAGCAGTAGGGGCAGGAGACAGCGTAGGGGAGAGGATGTGGTTCACCCTCTGAAGGTTTCTCTGGAGGAATTGTACAATGGCACATCAAAGAAGCT




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTACGGTGAAGATGCTCTCAAGGAGGGGATGGGTCCTGGTGGTGGGATGCATGACCCATTTGACATTTTTTCCTCATTCTTTGGAGGTGGCTTTGGAGgtacgagacatgagaagcagctcaattcaacctcctggtgattgtggtttgcttagattttgactggctctcattgtggtctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG