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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctgccttaacagtcaacacccccacaataaatgcatattctatgtagacatctgttggggaagttttgattagtagcctatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g51200.1
intron # 11
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|33679218|gb|CF307457.1|CF307457
EST:     TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTG                         GGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
genomic: TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGgtaagtctct ... tatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
EST: gi|66913357|gb|CX100205.1|CX100205
EST:     TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTG                         GGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
genomic: TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGgtaagtctct ... tatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
EST: gi|218488633|gb|FG946946.1|FG946946
EST:     TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTG                         GGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
genomic: TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGgtaagtctct ... tatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
EST: gi|33797259|gb|CF324492.1|CF324492
EST:     TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTG                         GGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
genomic: TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGgtaagtctct ... tatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
EST: gi|33678591|gb|CF306830.1|CF306830
EST:     TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTG                         GGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
genomic: TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGgtaagtctct ... tatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
EST: gi|33679446|gb|CF307685.1|CF307685
EST:     TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTG                         GGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC
genomic: TACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGgtaagtctct ... tatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGAC

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: 75 (upstream exon), 61 (downstream exon)
Score: 24

GTTTTCAGTTTGACTATGTGTTTGACTGGACAATACTGAAGTACCAGCAATCTCAAATTGCTAGTGCTCCACCCCGTGCAGTGgtaagtctct ... tatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catattctatgtagacatctgttggggaagttttgattagtagcctatgttgcagGGCCATGGTGCAGGACCTTCTGGGTTAGCACCACCAGCATTGCAAAACGACAGGCAGTCAG
                              ttttgat  putative branch site (score: 24)
                              ttttgatta  TA-rich tract