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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatccctttcttcacacatatgagctctgaatattccctggaacatttcatctctgaaaatcttcctaacaatgaatcaatgctctaatgaaaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCATAACGGATTCATCGGTATATGGATCGCATTAACGATCTACATGAGCCTGA

Basic information

species Oryza sativa
transcript LOC_Os03g11734.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11734.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G163154_T02 (Zea mays), 3'ss of exon 10
gtaaatccctttcttcacacatatgagctctgaatattccctggaacatttcatctctgaaaatcttcctaacaatgaatcaatgctctaatgaaaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCATAACGGATTCATCGGTATATGGATCGCATTAACGATCTACATGAGCCTGA
||||| | |||| | | || || | || | ||||| |||||||| |||||| ||||||||| | ||||| ||||| ||||||| ||| || || | || ||||| ||||| | ||||||||||| |||||||||||||||||||||||||||||||| |||||||||||||| ||||
gtaaactcttttcacatctcccattctgataaaaaagtc------aggtttcaactctgaaactcttcccaacaatgaaaatggacctgaatgagaatcttcagGTTGCTGTTGCGTCTGTGTCGATACCATGCCTGCTGTACCTTTCTGCGCATAACGGATTCATCGGTATATGGATCGCATTGACGATCTACATGAGTCTGA
















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|56550155|gb|CX056259.1|CX056259
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|89185192|gb|CI050926.1|CI050926
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|89184487|gb|CI047052.1|CI047052
EST:     ACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|86498292|gb|CI140925.1|CI140925
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|86430518|gb|CI082941.1|CI082941
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|86533629|gb|CI173835.1|CI173835
EST:     TGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: TGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|86497553|gb|CI140186.1|CI140186
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|86495252|gb|CI137885.1|CI137885
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|86430709|gb|CI083132.1|CI083132
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCGTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|88987299|gb|CI034266.1|CI034266
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|89194404|gb|CI116841.1|CI116841
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
EST: gi|88223496|gb|CI223345.1|CI223345
EST:     ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATG                         GTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT
genomic: ATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCAT

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: 31 (upstream exon), 62 (downstream exon)
Score: 2

TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccct ... aaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCATAACGGATTCATCGGTATATGGATCGCATTAACGATCTACATGAGCCTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcatctctgaaaatcttcctaacaatgaatcaatgctctaatgaaaatctccagGTTGGTGTGGCTGCTATCTCCATACCCTGCCTAGTATACCTTTCTGCTCATAACGGATTCATCGGTATATGGATCGCATTAACGATCTACATGAGCCTGA
                                                tctcc  CT-rich tract
 taatgaaaat  TA-rich tract