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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGTTTCGATGATGAGATGAGGACGGTTGTTGCAAGTAACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaagctgacatcctaaagtgcattttgattcccatgtgttctgttttcacgataggttttgatctgtttcttttttatgtaaaccag

Basic information

species Oryza sativa
transcript LOC_Os02g56850.1
intron # 9
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g56850.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G806449_T02 (Zea mays), 5'ss of exon 9
AGGTTTCGATGATGAGATGAGGACGGTTGTTGCAAGTAACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaagctgacatcctaaagtgcattttgattcc----catgtgttctgttttcacgataggttttgatctgtttctttt--ttatgtaaaccag---
|||||| ||||||||||||||  |  |||||||||| ||||||||||||||||||||||  || ||||||||||||||||| |||||||||| ||   ||||  | | | |||||||||||||| |    |||  |||||   ||   | |  ||||   | | |||       ||  ||||| | |   
AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgatttttactgaagtacaacagtgcattttgatttctaaacataagttctaagtt--gggtcagtttcattttattttaaccagttgagtaaaacggctg

upper sequence: LOC_Os02g56850.4 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM5G806449_T01 (Zea mays), 5'ss of exon 8
AGGTTTCGATGATGAGATGAGGACGGTTGTTGCAAGTAACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaagctgacatcctaaagtgcattttgattcccatgtgttctgttttcacgataggttttgatctgtttcttttttatgtaaaccag
|||||| ||||||||||||||  |  |||||||||| ||||||||||||||||||||||  || ||||||||||||||||| |||||||||| ||   ||||  | | | |||||||||||||| | |    |   ||| | |        || | || ||||| |||| || | ||||||
AGGTTTTGATGATGAGATGAGAGCTATTGTTGCAAGCAACCTTGAGGGAAGGGGAATCAAGTTGCATCCAGGGACAAATCTCTCTGAGgtgatttttactgaagtacaacagtgcattttgatttctaaacataa-gttctaag-------ttgggtcagtttcatttt-attttaaccag
















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|58692171|gb|CK080858.1|CK080858
EST:     ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAG                         TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
genomic: ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaag ... tgtaaaccagTTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
EST: gi|27578226|gb|CB000921.1|CB000921
EST:     ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAG                         TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
genomic: ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaag ... tgtaaaccagTTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
EST: gi|58601900|gb|CK012428.1|CK012428
EST:     ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAG                         TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
genomic: ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaag ... tgtaaaccagTTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
EST: gi|319908658|gb|HS977786.1|HS977786
EST:     ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAG                         TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
genomic: ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaag ... tgtaaaccagTTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAG
EST: gi|4714976|gb|AU056093.1|AU056093
EST:     ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAG                         TTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGGAGAGGA
genomic: ACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaag ... tgtaaaccagTTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGG-AGAGGA

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: 62

AGGTTTCGATGATGAGATGAGGACGGTTGTTGCAAGTAACCTTGAGGGAAGGGGAATCAGATTACATCCAGGGACAAATCTATCTGAGgtgagttaag ... tgtaaaccagTTGAGTAAAACAGCCGATGGCATAAAAGTTGTCACTGACAAAGGAGAGGAGATCATTGCAGATGTTGTTCTGTTTGCTACAG




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