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'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgcaaatctgtacttgttgagcatctggcattatgaactcactgttttaaatcctatgccatttgactaccaacttttactaaagagacatcgtgctatgcatatttagcacaaaaaaatgattttgtaaaacgtgataatgcataactcatgatgatccatccgtatccttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g09320.1
intron # 16
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|86519891|gb|CI160097.1|CI160097
EST:     GTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: GTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29668943|gb|CB665218.1|CB665218
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|58689010|gb|CK077697.1|CK077697
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCA-                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|218502213|gb|FG961004.1|FG961004
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29640538|gb|CB645547.1|CB645547
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|218490049|gb|FG963619.1|FG963619
EST:     CACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAAGCCAG                         G-TCGTGCAGTATTTGCCAGC
genomic: CACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGA-GCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGC
EST: gi|58604549|gb|CK015077.1|CK015077
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29642463|gb|CB647470.1|CB647470
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|218479902|gb|FG948663.1|FG948663
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|218493259|gb|FG949070.1|FG949070
EST:     CACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGNGAGCCA-                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAA
genomic: CACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTG-GAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAA
EST: gi|58671293|gb|CK059979.1|CK059979
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29630820|gb|CB635829.1|CB635829
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29663066|gb|CB659341.1|CB659341
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29625639|gb|CB630650.1|CB630650
EST:     GAAGCATATAACGGGAGCCGG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: GAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|58673473|gb|CK062159.1|CK062159
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|87041398|gb|CI196020.1|CI196020
EST:     GAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: GAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|58585822|gb|CF984130.1|CF984130
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29645566|gb|CB650573.1|CB650573
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29626361|gb|CB631372.1|CB631372
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|87041092|gb|CI195714.1|CI195714
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29681753|gb|CB678028.1|CB678028
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|29626362|gb|CB631373.1|CB631373
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|218502862|gb|FG946696.1|FG946696
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|88197857|gb|CI197707.1|CI197707
EST:     CTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|218497744|gb|FG966597.1|FG966597
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAACTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|88198739|gb|CI198589.1|CI198589
EST:     CACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|8956808|gb|BE230611.1|BE230611
EST:     CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAG                         GGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: CCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
EST: gi|86519039|gb|CI159245.1|CI159245
EST:     ACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGTAGCCAG                         GGTCGTCCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT
genomic: ACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAAT

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: 74 (upstream exon), 75 (downstream exon)
Score: 51

CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgca ... atccttgcagGGTCGTGCAGTATTTGCCAGCGGCAGTCCGTTTGACCCTGTGGAGTACAATGGAAAGATACATGTGCCAGGCCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGACCCGTCATTTTCTCTCTGTCAAACCCCACATCACACTCTGAGTGTACTGCTGAAGAAGCATATAATTGGAGCCAGgtgagctgcaaatctgtacttgttgagcatctggcattatgaactcactgttttaaatcctatgccatttgactaccaacttttactaaagagacatcgtgctatgcatatttagcacaaaaaaatgattttgtaaaacgtgataatgcataactcatgatgatccatccgtatccttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG