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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgatgcatgattctttttaccttctttttgtataattgacatggtctgaaatacagtgcattgtgaagtatatccgtataacctcttgctttatataaaaaatatttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g51220.1
intron # 3
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|88382318|gb|CI633176.1|CI633176
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATCCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88303013|gb|CI668859.1|CI668859
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88347620|gb|CI634305.1|CI634305
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGACAGACTCGACTGCCAGGTATATTATCGTTCACTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88336811|gb|CI644238.1|CI644238
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGANTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88356314|gb|CI652718.1|CI652718
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88338206|gb|CI633325.1|CI633325
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88575096|gb|CI666865.1|CI666865
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88305183|gb|CI651980.1|CI651980
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|109974426|gb|DT806902.1|DT806902
EST:     GTTATGCTGCTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGGTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88575793|gb|CI669938.1|CI669938
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATCCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|163929185|gb|EG713058.1|EG713058
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88719072|gb|CI742582.1|CI742582
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATCATCGTTCAT
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCAT
EST: gi|88381600|gb|CI682265.1|CI682265
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
EST: gi|88327973|gb|CI648377.1|CI648377
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAG
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAG
EST: gi|88308467|gb|CI650876.1|CI650876
EST:     GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAG                         GGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC
genomic: GTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGC

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: 64 (upstream exon), 75 (downstream exon)
Score: 35

GCTGGAAGATGCTGGTTATGCTGTTGGTGCAAGAGTTCTTGAACTACTCTGTCACAGAGAGAAGgtttgatgca ... tttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgaagtatatccgtataacctcttgctttatataaaaaatatttaattcagGGGAATAGGCGAGAGACTCGACTGCTAGGTATATTATCGTTCATTCACAGCACTGTATGGAAAGTTTTGTTTGGGAAG
                 tataacctcttgcttt  TA-rich tract