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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_Os01g73530.1
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

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: 71 (upstream exon), 59 (downstream exon)
Score: 16

ATTTCCTTCCATGATGTGGATATCGTAACGCCATCTCAAAAGCTATTGGCTACCCAGTTATCTTGTGATGTATCTCAAGGAAAAAGCCTTCTTGTGACTGgtacatcatc ... ttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGTGGCCCATCGCTTCAGGGAGGCTTACCATGCCGTCTGATGGCATCTTTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttactttcatgtttacattatatgttctaatatctatcatgctgttttcttaagGCCCAAATGGCAGTGGCAAGAGCTCCATTTTTAGGGTGCTCCGAGGTTTGTGGCCCATCGCTTCAGGGAGGCTTACCATGCCGTCTGATGGCATCTTTCA
                         ttctaat  putative branch site (score: 16)
                                          ctgttttctt  putative PPT
            tttacattatatgttc  TA-rich tract