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'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatcctgcgcgctcccctctctgcccccatcgttcaccctagaaccctaacggcgctgtttgctaaactgtttcccccctttggtttggttgttgtggcggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG

Basic information

species Oryza sativa
transcript LOC_Os03g21990.1
intron # 2
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|58662654|gb|CK051340.1|CK051340
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88424534|gb|CI608120.1|CI608120
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|29636115|gb|CB641124.1|CB641124
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88373248|gb|CI614584.1|CI614584
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGTTGGAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|87014311|gb|CI305089.1|CI305089
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|44679480|gb|CR292914.1|CR292914
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|29643708|gb|CB648715.1|CB648715
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|86903823|gb|CI302469.1|CI302469
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|58658761|gb|CK047441.1|CK047441
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|58593917|gb|CF992225.1|CF992225
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88355041|gb|CI615922.1|CI615922
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGGTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|58593323|gb|CF991631.1|CF991631
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|29633914|gb|CB638923.1|CB638923
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|29679952|gb|CB676227.1|CB676227
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88727351|gb|CI751006.1|CI751006
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|27577849|gb|CB000544.1|CB000544
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88337417|gb|CI629707.1|CI629707
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|58689854|gb|CK078541.1|CK078541
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88432601|gb|CI567640.1|CI567640
EST:     GAACTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTTGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88400765|gb|CI616770.1|CI616770
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88449555|gb|CI579835.1|CI579835
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88398052|gb|CI585555.1|CI585555
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATC-GGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88725912|gb|CI747424.1|CI747424
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88337391|gb|CI629681.1|CI629681
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|58694088|gb|CK082775.1|CK082775
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|117225886|gb|CT848635.1|CT848635
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|33653589|gb|CF276203.1|CF276203
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88315266|gb|CI611930.1|CI611930
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|58613176|gb|CK040888.1|CK040888
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|58660795|gb|CK049475.1|CK049475
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88402668|gb|CI598895.1|CI598895
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGCAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
EST: gi|88312303|gb|CI582641.1|CI582641
EST:     GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAG                         TAAGCAGGTTCGTGTCGGCTGGAAG
genomic: GACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG

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), 25 (downstream exon)
Score: 22

AGCCGCAGTCGCTGAAGAAGCTGAGCCTCAAGTCGCTCAAGCGCTCGCACGACCTCTTCGCGCCCACCCACTCCCTCCTCTTCACTCCCGATCCGGAGAGgtaaatcctg ... cggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgctgtttgctaaactgtttcccccctttggtttggttgttgtggcggacggcagTAAGCAGGTTCGTGTCGGCTGCAAG
       tgctaaa  putative branch site (score: 22)