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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagaattcagacatgtgaatctgtgacactcctcgttaattttaaacttggttatagtttgtttacgatatgagcttttgttactgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA

Basic information

species Oryza sativa
transcript LOC_Os01g22510.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g22510.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G113495_T01 (Zea mays), 3'ss of exon 5
gtgagaattcagacatgtgaatctgtgacactcctcgttaattttaaacttggttatagtttgtt-tacgatatgagcttttgttactgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
||||| |||||| |         ||||||| |  |  |||  || |       |  |  ||      | ||| |    |||  || ||    ||||||||||||||| ||||||||||||||||||||||| || ||||| |||
gtgagtattcagcc--------ttgtgacatttatttttaccttcaggtgacatgttccttcaaaacatgatcttccttttcattgctaaacgcagCTGACGGTGGCATATGAAGTTCCTGAAATTTTGGCCCCAGTTGCATCA
















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|58586474|gb|CF984782.1|CF984782
EST:     GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAA                         CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
genomic: GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
EST: gi|33816970|gb|CF334318.1|CF334318
EST:     GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAA                         CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
genomic: GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
EST: gi|33676318|gb|CF304557.1|CF304557
EST:     GGGTGCTGTTCGTTTCTTTCNTAAAAGCTCATCCTCTTGCAGAGTACAA                         CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
genomic: GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
EST: gi|18386325|gb|BM419524.1|BM419524
EST:     GGGTGCTGTTCGTTTCTTTCCTAAAAGCGTCATCCTCTTGCAGAGTACAA                         CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
genomic: GGGTGCTGTTCGTTTCTTTCCTAAAAGC-TCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
EST: gi|33675987|gb|CF304226.1|CF304226
EST:     GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAA                         CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
genomic: GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
EST: gi|87025583|gb|CI254629.1|CI254629
EST:     GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAA                         CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
genomic: GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
EST: gi|86852194|gb|CI319129.1|CI319129
EST:     CATCCTCTTGCAGA-TACAA                         CTGAC-GT-GCTTATGAAGTTCCT-AAATTTT-GCACCTGTTGCGTCA
genomic: CATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
EST: gi|33685901|gb|CF314140.1|CF314140
EST:     GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAA                         CTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
genomic: GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA

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: 49 (upstream exon), 49 (downstream exon)
Score: 16

GGGTGCTGTTCGTTTCTTTCCTAAAAGCTCATCCTCTTGCAGAGTACAAgtgagaattc ... ctgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttaaacttggttatagtttgtttacgatatgagcttttgttactgtctgcagCTGACGGTGGCTTATGAAGTTCCTGAAATTTTGGCACCTGTTGCGTCA
 cgttaat  putative branch site (score: 16)
             ttatagtttgttta  TA-rich tract