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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagacatgttttcaacgcatgcattccattttgcgcactccacaattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA

Basic information

species Oryza sativa
transcript LOC_Os03g57290.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 16
---------------gttagacatgttttcaacgcatgcattccattttgcgc---actcca-caattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA
                 ||   |  ||  |  || |||   |  |  |  ||    |||  | |    || |    ||    |  |||  | ||  |  |||||||||||||||||  | |||||| | |||||||||||||||||||||||| | |||||| |||||||||||||| | |||||||||||||||||||||||||
gtaactcttcagaatactaattaatttagctgcgtatgttattgacctcacggctaacttgaaccccctttaaccgttgggtttcatccatgtccctcatttcagCTCAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTGATCGACCGGGAGTACCTGGAGCGCGACAGGAGTAACCCCCAGATCTACA

upper sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: AC177936.6_FGT008 (Zea mays), 3'ss of exon 4
---------------gttagacatgttttcaacgcatgcattccattttgcgc--actccacaattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA
                |||   |  ||  |   | |||   |  |  || ||   |||  ||    || |    ||    |  |||  | ||| |  |||||||| ||||||||  | |||||| | |||||||||||||||||||||||| |||| ||| |||||||||||||| | |||||||||||||||||||||||||
gtgacacttcagaatattaattaatttagctgtgtatgttatttaccttacgacaacttgaccccctttaacctttggggttcatccatgtctctcatttcagCTTAAGTTCCCTGTTAAGCCAGCTGATATCAAGAAAAGAATAGAGAGCTTAATAGACCGGGAGTACCTGGAGCGGGACAGGAGTAACCCCCAGATCTACA

upper sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA15G10030.1 (Glycine max), 3'ss of exon 16
---------gttagacatgttttcaacgcatgcattccattttgcgcac--tccacaattt--tgatatcttaaaatatatcgttttcttttcttt-cagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA
           || |  || | ||     || ||  |  ||||        |  | || ||  |  ||  ||||   |     |||| || | |   |||||||| || ||||| || ||| | ||  | |||||||| || || ||||| || ||||||||||| ||||||||||||| ||  ||||| || || ||||
gttgtgtacaatacaagtgatctcttttgatacagactgttttctctctgattgataagttaatactaatttaaggaagtgaatttttttgtgtgaacagCTCAAATTTCCAATAAAACCAGCTGACTTGAAGAAAAGGATCGAAAGCCTGATTGACAGGGAGTATCTGGAGAGAGACAAGAACAACCCTCAAATATACA

upper sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ14633 (Selaginella moellendorffii), 3'ss of exon 16
gttagacatgttttcaacgcatgcattccattttgcgcactccacaattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA
               || || ||  | |  ||    | | |      |   ||     ||   ||| |  |||| | |     |||||||||||||| || |||||| ||||  | |||||| | || |||||||| |||||| | |||||| ||||| |||||| ||  ||||| ||| | ||||
-------------gtaaggcctggctgctgtt----ggaat--gtggtgccgacgctgta---tatgtt-ttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

upper sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 16
lower sequence: EFJ26297 (Selaginella moellendorffii), 3'ss of exon 16
gttagacatgttttcaacgcatgcattccattttgcgcactccacaattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA
               || || ||  | |  ||    | | |      |   ||         |||| |  |||| | |     |||||||||||||| || |||||| ||||  | |||||| | || |||||||| |||||| | |||||| ||||| |||||| ||  ||||| ||| | ||||
-------------gtaaggcctggctgctgtt----ggaat--gtggtgccgacgct---ggatatgtt-ttttgtgtgtgaccagCTCAAGTTCCCTATAAAGCCAGCGGACTTGAAGAAACGTATCGAGAGCCTGATCGACCGCGAGTACTTGGAGCGAGACAAGAACAACCCTCAGGTATACA

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|218499064|gb|FG952650.1|FG952650
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|87029771|gb|CI274452.1|CI274452
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|58694714|gb|CK083401.1|CK083401
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|87013825|gb|CI271216.1|CI271216
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|86889987|gb|CI319976.1|CI319976
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|58684068|gb|CK072755.1|CK072755
EST:     CACGT-AAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|89187076|gb|CI047143.1|CI047143
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|86482476|gb|CI125109.1|CI125109
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|38568751|gb|CD670966.1|CD670966
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|89178617|gb|CI391615.1|CI391615
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|89189344|gb|CI048883.1|CI048883
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|58658824|gb|CK047504.1|CK047504
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|58658361|gb|CK047041.1|CK047041
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|88844604|gb|CI020451.1|CI020451
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|88837448|gb|CI078808.1|CI078808
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|86535745|gb|CI175951.1|CI175951
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
EST: gi|89181587|gb|CI113093.1|CI113093
EST:     CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAG                         CTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA
genomic: CACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTA

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: 65 (upstream exon), 70 (downstream exon)
Score: 44

GTGGATGCTGCCATAGTTCGAATAATGAAGACACGTAAAACCCTCAGCCACACGCTTCTAATAACTGAGCTTTTTCAGCAGgttagacatg ... tttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgcgcactccacaattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA
                ttttgat  putative branch site (score: 44)
                                tatatcgttttctttt  putative PPT
              aattttgatatcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagacatgttttcaacgcatgcattccattttgcgcactccacaattttgatatcttaaaatatatcgttttcttttctttcagCTCAAGTTCCCAATCAAGCCATCGGATATCAAGAAAAGAATAGAGAGCCTAATCGACAGGGAGTACCTGGAGAGAGACAGGAGTAACCCCCAGATCTACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA