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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTCCTCTGATCATCGGGTGCGACGTGAGGCACATGTCGCAGGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctactcttcctgctgccgcgagcttcaggaattcagagagttttcatggcgcttgtcggattgatctttttgggaattcag

Basic information

species Oryza sativa
transcript LOC_Os10g35070.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g35070.1 (Oryza sativa), 5'ss of exon 12
lower sequence: GRMZM2G095126_T02 (Zea mays), 5'ss of exon 10
GCTCCTCTGATCATCGGGTGCGACGTGAGGCACATGTCGCAGGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgta------ctctact-cttcctgctgccgcgagcttcaggaattcagagagttttcatggcgc-ttgtcggattgatcttt-ttgggaattcag--------------
|| ||||| |||||||| |||||||| ||||||||||||| ||||||||||| ||||||||||||||||||||| ||||||||||||||||||       | |  || | | | ||  ||||| |         ||||  ||        |  || ||||     || | | | |||||  | |                
GCGCCTCTCATCATCGGCTGCGACGTCAGGCACATGTCGCGGGAGACGTACGCCATCCTGGCCAACAAGGAGGTGATCGCCGTCAACCAAGgtgagagcgcccggctgcgttcagcgcccgcgtgtccagttttttcactgaccggaggcgatgcgttgttcctgtgttgtgtgttgggcgtgcgtcgcgtcgcgtgcag
















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|86493490|gb|CI136123.1|CI136123
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86495134|gb|CI137767.1|CI137767
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86494558|gb|CI137191.1|CI137191
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|29636610|gb|CB641619.1|CB641619
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|218485187|gb|FG948602.1|FG948602
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86428613|gb|CI075294.1|CI075294
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTTATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86492659|gb|CI135292.1|CI135292
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|87028082|gb|CI257242.1|CI257242
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGC
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86412949|gb|CI067354.1|CI067354
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86537386|gb|CI177592.1|CI177592
EST:     AACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: AACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|87007083|gb|CI277158.1|CI277158
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86502730|gb|CI145363.1|CI145363
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86493677|gb|CI136310.1|CI136310
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
EST: gi|86496055|gb|CI138688.1|CI138688
EST:     GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAG                         ATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG
genomic: GGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGG

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: 61 (upstream exon), 71 (downstream exon)
Score: 39

GCTCCTCTGATCATCGGGTGCGACGTGAGGCACATGTCGCAGGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctact ... gggaattcagATGCTCTGGGCATCCAGGGGAAGAAGGTGAGGATGGAGGGCAGCAGCGAGGTGTGGGCGGCGCCGCTGTCGGGTTACAGGACGGCGGTGCTGCTGCTGAA




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTCCTCTGATCATCGGGTGCGACGTGAGGCACATGTCGCAGGAGACGTACGACATCCTGGCCAACAAGGAGGTCATCGCCGTCAACCAAGgtactctactcttcctgctgccgcgagcttcaggaattcagagagttttcatggcgcttgtcggattgatctttttgggaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG