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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaagccttccttgtgcctggtgagaaggttcatagcttcaggggtttagtgctctcattttaacacggcaccatgctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGACAAGAGGACAGCCTGAGAGAGTCTGCACGCACATGCACATGCAACCTTC

Basic information

species Oryza sativa
transcript LOC_Os02g57710.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57710.1 (Oryza sativa), 3'ss of exon 13
lower sequence: GRMZM2G096343_T01 (Zea mays), 3'ss of exon 13
--------------------------------------gtaagtaa-agccttccttg---tgcctggtgagaaggttcatagcttcagg----ggtttagtgctct---cattttaacacggcaccatgctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGACAAGAGGACAGCCTGAGAGAGTCTGCACGCACATGCACATGCAACCTTC
                                      ||| |||  ||  || | ||   || ||  ||   |||||| |   ||   |    | | || || | |     ||||||||    ||||   |  ||||||||||||| |||| || |||| |||  | || || ||||| ||||| ||||||| ||||||||| |||||||| |||||||||||||||      ||   
gtaagtgatgcctgcccctgacgatagtatctatctatgtatgtaggagtatttcatgccatgtcttctggataggttcctgtttttttgttttgttctattgttttgtttgttttaacaaaataccaaatttgtgcagGCACCTTCTTAGCACTGGGCATGAAGAGAGGCGAGCTCAGAAACCTGTGGACAAAAGGACAGCCCGAGAGAGTGTGCACGCACATGCACCCATCCCCCAA
















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|29613255|gb|CB618268.1|CB618268
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|58653658|gb|CK042338.1|CK042338
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|29623067|gb|CB628078.1|CB628078
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|29632359|gb|CB637368.1|CB637368
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|29639825|gb|CB644834.1|CB644834
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|29631554|gb|CB636563.1|CB636563
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|58658945|gb|CK047625.1|CK047625
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|29676694|gb|CB672969.1|CB672969
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|29677467|gb|CB673742.1|CB673742
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|89188671|gb|CI115920.1|CI115920
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|86833256|gb|CI334851.1|CI334851
EST:     TTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCATGAACCTCTGGA
genomic: TTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|58679622|gb|CK068309.1|CK068309
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|29628485|gb|CB633496.1|CB633496
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|88273413|gb|CI393819.1|CI393819
EST:     GATGGTCATGGTCAACCAGCTCTTCTTTACATTGTCCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|58659339|gb|CK048019.1|CK048019
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|33798918|gb|CF325316.1|CF325316
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|18386669|gb|BM419867.1|BM419867
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
EST: gi|88967262|gb|CI002456.1|CI002456
EST:     GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTG                         GCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA
genomic: GGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGA

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), 72 (downstream exon)
Score: 52

GTCTTATGATCACGTATGTTGCCTTGAACCTTATGGATGGTCATGGTCAACCAGCTCTTCTTTACATTGTGCCTTTTACGCTTGgtaagtaaag ... gctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGACAAGAGGACAGCCTGAGAGAGTCTGCACGCACATGCACATGCAACCTTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatagcttcaggggtttagtgctctcattttaacacggcaccatgctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGACAAGAGGACAGCCTGAGAGAGTCTGCACGCACATGCACATGCAACCTTC
                            ttttaac  putative branch site (score: 52)
                         tcattttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtaaagccttccttgtgcctggtgagaaggttcatagcttcaggggtttagtgctctcattttaacacggcaccatgctactgcagGCACCTTCATAGCGCTCGGCAGGAAACGGGGTGAACTCAGGAACCTCTGGACAAGAGGACAGCCTGAGAGAGTCTGCACGCACATGCACATGCAACCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA