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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTAAGCACTGAGCAGCAGTATGCCTTGGACCCCTTTGTACTCGACTTATTACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctcttgatctcctgaaacctttcatattcatgataatagaatctcataattctcactgaatttttaattttccatgcattgcag

Basic information

species Oryza sativa
transcript LOC_Os01g43680.1
intron # 2
splice site 5'
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|88736109|gb|CI759617.1|CI759617
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACA
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACA
EST: gi|88358481|gb|CI617567.1|CI617567
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAA
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAA
EST: gi|88389165|gb|CI597963.1|CI597963
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTT
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTT
EST: gi|88364938|gb|CI616357.1|CI616357
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCC
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCC
EST: gi|88371295|gb|CI600143.1|CI600143
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
EST: gi|88719728|gb|CI743238.1|CI743238
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTG
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTG
EST: gi|88431664|gb|CI576855.1|CI576855
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
EST: gi|88729836|gb|CI753057.1|CI753057
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAAT
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAAT
EST: gi|88317350|gb|CI627999.1|CI627999
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTG
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTG
EST: gi|88330923|gb|CI638331.1|CI638331
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
EST: gi|88732428|gb|CI755605.1|CI755605
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTT
EST: gi|88391747|gb|CI603266.1|CI603266
EST:     TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGT                         GTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTT
genomic: TACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTT

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: 58 (upstream exon), 75 (downstream exon)
Score: 20

CTTAAGCACTGAGCAGCAGTATGCCTTGGACCCCTTTGTACTCGACTTATTACAGCAGCCGAAAGTCTGTTCACCTTGCTGTGTTTTTCCGTGTGATTGTgtatgtctct ... tgcattgcagGTGAGGCGGTCACATTTACAGGAGAATCCTTTTCCTTTGTGGTTCTTTGTTCTTGACGACATTGGGTGTGTAAAAATTGAGAATGTATGTTAAGGTTGAA




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