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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GACTGCTAATGAAAATGGAGGTGAAACAACCTTCAGCTATGATCGGCTGATATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttattttccttgcaaccttggaagcaaagtaggtgttatgtgttgtttctgctaccttgtgaaatggataagcacttaccttacccataaatatg...

Basic information

species Oryza sativa
transcript LOC_Os03g24220.2
intron # 23
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24220.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G081322_T01 (Zea mays), 5'ss of exon 23
GACTGCTAATGAAAATGGAGGTGAAACAACCTTCAGCTATGATCGGCTGATATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttattttccttgcaaccttggaagcaaagtaggtgttatgtgttgtttctgctacct--------tgtgaaatggataagcacttaccttacccataaatatg
 || ||||| |||||||||||  | |||||||| |||||||| ||  |||||||||| || ||  |||||||| |||||||| |  |||| ||||||||||||||| | |  |  |||| | |||  |  |          | | | |   | ||| |||||        ||||||| || | || | ||  |  |   | |      
AACAGCTAAAGAAAATGGAGGCCAGACAACCTTTAGCTATGAACGATTGATATCAAAGTCCACTGACCCTGTTAGTGGGATAAACAACAAGCGCAGAGAGgtttgtgactc-cactgca-cattgataaaagctctctctctctctctctctcctgttacctcatttgcttgtgaaagggctgagtatttgtcgaaattaga------

upper sequence: LOC_Os03g24220.1 (Oryza sativa), 5'ss of exon 23
lower sequence: GRMZM2G359566_T01 (Zea mays), 5'ss of exon 8
GACTGCTAATGAAAATGGAGGTGAAACAACCTTCAGCTATGATCGGCTGATATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttattttccttgcaaccttggaagcaaag-taggtgttatgtgttgtttctgctaccttgtgaaatggataagca-cttaccttacccataaatatg
 |||||||| ||||| |||||  | || ||||| ||||| || ||  || ||||||| |||||  |||||||  ||||||||||  |||| ||||||||||||||| |||  |  |||  |||||  |  |    |   | |    | ||   ||   | | |||||  | || | ||    ||  | ||   | | || | 
AACTGCTAACGAAAACGGAGGCCAGACCACCTTTAGCTACGACCGCTTGGTATCAAAGTCTACTGACCCTGTCAGTGGGATAGACCACAAGCGCAGAGAGgtttgtgattcccactgcttccttgagaaaagctctctatctctcctattacctc-atttcgttgtgtgagggctgagtggtttgtcgtaattacacatgt-
















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|86479401|gb|CI122034.1|CI122034
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|16754192|gb|BM038571.1|BM038571
EST:     TCTACCAACCCTGTTCGTGGGATAGATTCCCAACCCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86479378|gb|CI122011.1|CI122011
EST:     TATCGAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|87022895|gb|CI269831.1|CI269831
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|89193062|gb|CI050360.1|CI050360
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86597638|gb|CI274629.1|CI274629
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86437319|gb|CI119041.1|CI119041
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|218505177|gb|FG951529.1|FG951529
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86502671|gb|CI145304.1|CI145304
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|29669713|gb|CB665988.1|CB665988
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86480869|gb|CI123502.1|CI123502
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTTGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|58667525|gb|CK056211.1|CK056211
EST:     AGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATGACGAAGGAA
genomic: AGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|9864985|gb|AU100735.1|AU100735
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTAC-AACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86252596|gb|CI003932.1|CI003932
EST:     TTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|86480878|gb|CI123511.1|CI123511
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|88260846|gb|CI361434.1|CI361434
EST:     CAACCCTGTTCCTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: CAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
EST: gi|29674448|gb|CB670723.1|CB670723
EST:     TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAG                         ACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA
genomic: TATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAA

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: 73 (upstream exon), 71 (downstream exon)
Score: 67

GACTGCTAATGAAAATGGAGGTGAAACAACCTTCAGCTATGATCGGCTGATATCAAAATCTACCAACCCTGTTCGTGGGATAGATTACAAACGCAGAGAGgtttgttatt ... gcttctgcagACATATTTGTCGGACAGCGAATTCCAGACTGTATTTGGTATAACGAAGGAAGAGTTCTACCAGCAGCCAGGGTGGAAACAAGAACTACAGAAAAGGAAGC




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