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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattgtctatagttatctttcagtagttgtttgtgcagttttggtattcatgctactttcctttattgatggttggtgccatttatttttccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC

Basic information

species Oryza sativa
transcript LOC_Os01g59930.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g59930.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G133213_T01 (Zea mays), 3'ss of exon 1
--cattgtcta-----tagttatctttcagtagttgtttgtgcagttttggtattcatgctactttcctttattgatggttggtgccatttatttttccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC
   ||   | |     || || |  || |||  ||| || |||| ||   |  || ||||    |  ||  |||  || ||| ||     | || ||    | | |||||| ||||||||||||||||||| |||||| |||||||| ||||||||||||||||||||||| || ||||| ||||| || |||||||||||||||||
tttatcacccaaaaaatatttgtgcttaagt--ttgcttctgcaattcaag-gttaatgcgttatagctcaatt--tgattgttgt--gctgttgttttggcattagGCTGCTTGGATCCTGAGAACTTCAGGAAGTTCAAACTTGTTGAAAAGAAGCAAATAAGTCATAATGTTGCCAGGTTCAAGTTCGCTCTTCCAACTCCAAC
















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|88362855|gb|CI614211.1|CI614211
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88763102|gb|CI772658.1|CI772658
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|58685456|gb|CK074143.1|CK074143
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|58684839|gb|CK073526.1|CK073526
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88736272|gb|CI759780.1|CI759780
EST:     GTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCCAAGG                         -CTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAG
genomic: GTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCC-AAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAG
EST: gi|58595179|gb|CF993487.1|CF993487
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88388215|gb|CI627754.1|CI627754
EST:     GGTCGCCGCGGGCGGGGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|2309816|gb|C25971.1|C25971
EST:     GGTCGCCGCGNGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGNTCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|25801449|gb|CA757410.1|CA757410
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|58603188|gb|CK013716.1|CK013716
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|427743|gb|D23879.1|D23879
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|88391603|gb|CI600792.1|CI600792
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
EST: gi|117244284|gb|CT843075.1|CT843075
EST:     GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGG                         GCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC
genomic: GGTCGCCGCGGGCGGCGCCTTCCTCCTCCTCCGGTCCAGGAAGCCCAAGGgtatgtattg ... ccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcatgctactttcctttattgatggttggtgccatttatttttccctcctcagGCTGTTTGGATCCTGAGAACTTCAAGAAGTTTAAACTTGTGGAAAAGAAGCAAATAAGTCATAACGTGGCCAGATTCAAATTTGCTCTTCCAACTCCAAC
                  tattgat  putative branch site (score: 3)
                               tgccatttatttttcc  putative PPT
                                   atttattttt  TA-rich tract