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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatccgtcttctagctattttcatatttaggttggattgattttccttataacactgatacatctatgatctatcttattctcttctcatgtactccttatatttacttgttaaaagtatcactgctaacaacattgactttgctccttctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCTCAAACTCAAACAG

Basic information

species Oryza sativa
transcript LOC_Os12g06890.1
intron # 5
splice site 3'
intron type U2

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|2310523|gb|C26678.1|C26678
EST:     CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCA                         ACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
genomic: CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCAgtaagcatcc ... tctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
EST: gi|33678464|gb|CF306703.1|CF306703
EST:     CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCA                         ACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
genomic: CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCAgtaagcatcc ... tctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
EST: gi|218497860|gb|FG958963.1|FG958963
EST:     CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCA                         ACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
genomic: CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCAgtaagcatcc ... tctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
EST: gi|58655133|gb|CK043813.1|CK043813
EST:     CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCA                         ACGGCGTTTCAACAATCTGACCCTACTCCAAGCATGTTCTCCTTCCAACCT
genomic: CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCAgtaagcatcc ... tctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
EST: gi|33794845|gb|CF323302.1|CF323302
EST:     CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCA                         ACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
genomic: CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCAgtaagcatcc ... tctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
EST: gi|58676341|gb|CK065028.1|CK065028
EST:     CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCA                         ACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT
genomic: CTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCAgtaagcatcc ... tctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCT

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), 60 (downstream exon)
Score: 27

ATTGAGCACTCCAGCTTTCTCTACTGGAAGCCTATTCAGCACACCTACCCCTGGAATGACTGGTGGACTGTTTGGCAGCATGTCTTCACCCTTTTCATCAgtaagcatcc ... tctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCTCAAACTCAAACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacttgttaaaagtatcactgctaacaacattgactttgctccttctgattcagACGGCGTTTCAACAATCTGCCCCTACTCCAAGCATGTTCTCCTTCCAACCTCAAACTCAAACAG
                                   ctttgctccttct  CT-rich tract
       ttaaaagtat  TA-rich tract