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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagtttttcatcctcacctgactagcattttcttctttacctcttatttttgggtcaaaggcggagatcttattataaaccttggagttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g01670.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g01670.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G135052_T01 (Zea mays), 5'ss of exon 3
TTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagtttttcatcctcacctgactagcattttcttctttacctcttatttttgggtcaaaggcggagatcttattataaaccttggagttcttgcag
||||||||||||||||||||||||||||| |||||||||||||| ||||||||||| || ||||| || |||||||| ||||| ||  |||||||||  || |||     |||  |  | | | | |||| |  ||               |    | | |     |  ||| ||||   |    ||    | |||||
TTTTTGAAGGTTCAAAAGAATGGAACAGGTGAGCATTTGCCCCCACCTAGGCCAAAGCGAAAGGCTGCCCATCCATATCCACACAAGTCCTCAAAAAAGGgtaag-----catttttccttaatttgcatctggtt-----------gccatgaaattacaatgatatgtctaattacggaagccgggaaacatgcag
















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|33686829|gb|CF315068.1|CF315068
EST:     GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAG                         CCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
genomic: GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
EST: gi|29664971|gb|CB661246.1|CB661246
EST:     GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAG                         CCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
genomic: GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
EST: gi|88725670|gb|CI748929.1|CI748929
EST:     GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAG                         CCCCTCAAGTTG
genomic: GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTG
EST: gi|29665005|gb|CB661280.1|CB661280
EST:     GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAG                         CCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
genomic: GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
EST: gi|33674838|gb|CF303077.1|CF303077
EST:     GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAG                         CCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
genomic: GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
EST: gi|117235846|gb|CT847813.1|CT847813
EST:     GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAG                         CCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
genomic: GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
EST: gi|29625024|gb|CB630035.1|CB630035
EST:     GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAG                         CCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT
genomic: GCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCT

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: 60 (upstream exon), 53 (downstream exon)
Score: 13

TTTTTGAAGGTTCAAAAGAATGGAACAGGCGAGCATTTGCCCCCTCCTAGGCCAAAACGGAAGGCAGCACATCCATACCCACATAAAGCCTCAAAAAGAGgcaagttttt ... gttcttgcagCCCCTCAAGTTGTCCTACCACAACAAGCTTCTCATCTAATGGAGCAAGGCTGTCTTATACCTATGGACATATCTCCTGTTGCTAGAAACTTTAATGCAAA




<











<


<