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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccctttcttcacacatatgagctctgaatattccctggaacatttcatctctgaaaatcttcctaacaatgaatcaatgctctaatgaaaatctccag

Basic information

species Oryza sativa
transcript LOC_Os03g11734.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g11734.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G163154_T02 (Zea mays), 5'ss of exon 10
TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccctttcttcacacatatgagctctgaatattccctggaacatttcatctctgaaaatcttcctaacaatgaatcaatgctctaatgaaaatctccag
|||||||| || || ||||| || ||||| || ||||||||||| |||||||||||||| ||||| |||||||||| |||||| |||||||||||||||||  | ||||    | |  ||        || | ||      |  ||||| |||||||| |||||| |||||||||      |   ||||| ||||| |||
TTTGTCGCCGGGACGCAGACCATCAATTCCCTGGCCTTCGTGTTTGATGGCATCAACTTTGGAGCGTCAGACTACAGATACTCTGCTTACTCCATGgtaaactcttttcacatctcccattctgataaaaaagtc------aggtttcaactctgaaactcttcccaacaatgaaaatggacctgaatgagaatcttcag

upper sequence: LOC_Os03g11734.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G418400_T01 (Zea mays), 5'ss of exon 5
TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccctttcttcacacatatgagctctgaatattccctggaacatttcatctctgaaaatcttcctaacaatgaatcaatgctctaatgaaaatctccag-
|||||| ||||||| ||||| || ||||| || |||||| |||| |||||||||||||| ||||| |||||||||| |||||| |||||||||||||||||   || | ||||||  |   |  ||||| ||      |  |  ||||| |||| ||| |||||| |||||||||      |   ||||| || || ||| 
TTTGTCACTGGCACGCAGACCATCAATTCCCTGGCCTTCATGTTTGATGGCATCAACTTTGGAGCGTCAGACTACAGATACTCTGCTTACTCCATGgtaaa---ctcttttcacatctccca-ttctga-tagaaaaagtcaggtttcagctctaaaactcttcccaacaatgaaaatgaaccagaatgagaaacttcagg
















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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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGTCGCTGGCACACAGACGATAAATTCACTAGCCTTCGTGTTCGATGGCATCAACTTCGGAGCATCAGACTACACATACTCAGCTTACTCCATGgtaaatccctttcttcacacatatgagctctgaatattccctggaacatttcatctctgaaaatcttcctaacaatgaatcaatgctctaatgaaaatctccag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT