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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggacatttgatagttcatagtactatcttgtgttccccaatatggcgttgagttaaattattgttgttttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG

Basic information

species Oryza sativa
transcript LOC_Os01g13190.1
intron # 7
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|32948183|gb|BP184755.1|BP184755
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|29680232|gb|CB676507.1|CB676507
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|29685418|gb|CB681693.1|CB681693
EST:     TGCTNNNNNNNGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: TGCT-AAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|88422364|gb|CI689178.1|CI689178
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|58678012|gb|CK066699.1|CK066699
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|58673757|gb|CK062443.1|CK062443
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAGGT
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAGGT
EST: gi|29683233|gb|CB679508.1|CB679508
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|29662201|gb|CB658476.1|CB658476
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATG
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATG
EST: gi|87017573|gb|CI289706.1|CI289706
EST:     TGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: TGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|58666767|gb|CK055453.1|CK055453
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
EST: gi|88583475|gb|CI700958.1|CI700958
EST:     GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAG                         GCCATTTCAGCCATGGCATGGGGAACAGTCTC
genomic: GTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTC

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: 63 (upstream exon), 42 (downstream exon)
Score: 15

GAGGTTCTTTACTGTGCTAAAAAAGCTGGTGTGACACATGTATTGAAAGCTGGAGGAGCTCAGgtaggacatt ... tttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatcttgtgttccccaatatggcgttgagttaaattattgttgttttctttcagGCCATTTCAGCCATGGCATGGGGAACAGTCTCATGCCCAAAG
                                      ttgttgttttctttc  CT-rich tract
                              ttaaattattgttgtt  TA-rich tract