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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatcatctggcagcttttcgtcctagcttttatttactttcatgtttacattatatgttctaatatctatcatgctgttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGTGGCCCATCGCTTCAGGGAGGCTTACCATGCCGTCTGATGGCATCTTTCA

Basic information

species Oryza sativa
transcript LOC_Os01g73530.2
intron # 21
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g73530.1 (Oryza sativa), 3'ss of exon 21
lower sequence: GRMZM2G074241_T01 (Zea mays), 3'ss of exon 4
gta-catcatctggcagcttttcgtcctagcttttatttactttca---tgtttacattatatgttctaatatctatcatg----ctgttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGTGGCCCATCGCTTCAGGGAGGCTTACCATGCCGTCTGATGGCATCTTTCA
|||  |||||   ||||| |||    |  | ||  || ||| | |    || | ||||  | |  |||||| ||| | |||     ||||   | |||| |||||||| || || ||||| ||||| ||||||||||| ||||| ||||||||||| ||||| || || |||| || ||| ||||| || || ||| |
gtaatatcatgctgcagcgttt--gtcgggtttaaatctacctgcgccctgctgacatggttt-ctctaatctctgttatggtttttgttccttgaagGTCCAAATGGTAGCGGAAAGAGTTCCATCTTTAGGGTGCTTCGAGGCTTGTGGCCCATTGCTTCTGGTAGTCTTAGCAAGCCATCTGAAGGAATTTTTAA
















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|33796779|gb|CF324255.1|CF324255
EST:     TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTG                         GCCCAAATGGCAGTGGCAAGAGCTCCATTTTTA
genomic: TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTGgtacatcatc ... ttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTA
EST: gi|8955961|gb|BE229765.1|BE229765
EST:     TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAA-CCTTCTTGTGACTG                         GCCCAAATGGCAGTGGCAAGANCTCCATTTT-AGGGTGCTCCGAAGTTTGT
genomic: TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTGgtacatcatc ... ttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGT
EST: gi|88434594|gb|CI690870.1|CI690870
EST:     TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTG                         GCCCAAATGGC
genomic: TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTGgtacatcatc ... ttttcttaagGCCCAAATGGC
EST: gi|58679369|gb|CK068056.1|CK068056
EST:     TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTG                         GCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGT
genomic: TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTGgtacatcatc ... ttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGT
EST: gi|33684550|gb|CF312789.1|CF312789
EST:     TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTG                         GCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGT
genomic: TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTGgtacatcatc ... ttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGT
EST: gi|58601488|gb|CK012016.1|CK012016
EST:     TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTG                         GCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGT
genomic: TACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTGgtacatcatc ... ttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactttcatgtttacattatatgttctaatatctatcatgctgttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGTGGCCCATCGCTTCAGGGAGGCTTACCATGCCGTCTGATGGCATCTTTCA
                         ttctaat  putative branch site (score: 2)
                                          ctgttttctt  putative PPT
            tttacattatatgttc  TA-rich tract