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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCACCTGCATTAGCCTTGGCAGCGTCGGTCTTGTTCTATCAATTGCAGTCCCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGCgtatgtctctgcaactctatagcagaaatttagaatgaaatttccaggtcaaatgtagtaacctgtcccttcttgatggttcag

Basic information

species Oryza sativa
transcript LOC_Os11g32320.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os11g32320.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G059252_T01 (Zea mays), 5'ss of exon 3
GCACCTGCATTAGCCTTGGCAGCGTCGGTCTTGTTCTATCAATTGCAGTCCCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGCgtatgtctct--gcaactcta-tagcagaaatttagaatgaaat-ttccaggtcaaatgtagtaacctgtcccttcttgatgg---ttcag
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GCACCTGCATTAGCCTCGGGAGTGTCGGGCTTGTTCTATCAATCGCTGTCCCAGAAGGTGGCAACAACTGGTTCTGGCTCATGACCCTGAGCCCCTTGGCgtatgtctctctgctactcaactcccagcaattcagaatgaattcttccagtacaaatgcagtaac-tgacccttcatgatgaggtcccag
















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|38471894|gb|CF956025.1|CF956025
EST:     GGCTTATGACCTTAAGCCCATTGGC                         GGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
genomic: GGCTTATGACCTTAAGCCCATTGGCgtatgtctct ... gatggttcagGGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
EST: gi|88366347|gb|CI553745.1|CI553745
EST:     CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGC                         GGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
genomic: CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGCgtatgtctct ... gatggttcagGGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
EST: gi|112785406|gb|EE590619.1|EE590619
EST:     CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGC                         GGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
genomic: CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGCgtatgtctct ... gatggttcagGGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
EST: gi|88384761|gb|CI556639.1|CI556639
EST:     CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGC                         GGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
genomic: CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGCgtatgtctct ... gatggttcagGGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
EST: gi|88289987|gb|CI547624.1|CI547624
EST:     CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGC                         GGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
genomic: CCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGCgtatgtctct ... gatggttcagGGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
EST: gi|88322957|gb|CI548051.1|CI548051
EST:     ACCTTAAGCCCATTGGC                         GGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA
genomic: ACCTTAAGCCCATTGGCgtatgtctct ... gatggttcagGGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAA

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: 75 (upstream exon), 75 (downstream exon)
Score: 65

GCACCTGCATTAGCCTTGGCAGCGTCGGTCTTGTTCTATCAATTGCAGTCCCGGAGGGTGGCAACAACTGGTTCTGGCTTATGACCTTAAGCCCATTGGCgtatgtctct ... gatggttcagGGGTGTATACTACTGGACAAAGGCATCAAGAAAAGAAGAGATCAAGGTCAAAATGATTTTATCGGATGACGGGAATGTATCCGAAATTCTTGTGCGGGGT




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