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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagcctttgtatgttattgctgcacttcaatttgctaactggaggaaatgatgtactcattatttggcaaaattattacttatcatgctctttcactt...

Basic information

species Oryza sativa
transcript LOC_Os04g46390.3
intron # 4
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|29644137|gb|CB649144.1|CB649144
EST:     GAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: GAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29639999|gb|CB645008.1|CB645008
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29643236|gb|CB648243.1|CB648243
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29643291|gb|CB648298.1|CB648298
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29678521|gb|CB674796.1|CB674796
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|14714017|gb|AU197958.1|AU197958
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29668764|gb|CB665039.1|CB665039
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|33654740|gb|CF277354.1|CF277354
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTAATGGTTGTCATGGTG
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTA-TGGTTGTCATGGTG
EST: gi|29637040|gb|CB642049.1|CB642049
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29645124|gb|CB650131.1|CB650131
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29657304|gb|CB653579.1|CB653579
EST:     ATGAAGAAACTATCCTTATCACGAAATATTCTGTGCCCCAAGTGCAAAGG                         AAAAGGGACCA
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCA
EST: gi|33657288|gb|CF279902.1|CF279902
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTAATGGTTGTCATGGTG
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTA-TGGTTGTCATGGTG
EST: gi|29614042|gb|CB619055.1|CB619055
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29683515|gb|CB679790.1|CB679790
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29680639|gb|CB676914.1|CB676914
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
EST: gi|29670817|gb|CB667092.1|CB667092
EST:     ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGG                         AAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT
genomic: ATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGT

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), 74 (downstream exon)
Score: 357

ATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagccttt ... ctgctttcagAAAAGGGACCAAATCTGAGGCTCCAGCAACATGCTATGGTTGTCATGGTGTAGGAATGAGGAATATAATGCGACAGATAGGACTAGGCATGATTCAACAT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATGTGGCGCATACTTTGAAGGTGTCTTTAGAAGATGTGTATAATGGATCTATGAAGAAACTATCATTATCACGAAATATTCTGTGCCCAAAGTGCAAAGGgtaagcctttgtatgttattgctgcacttcaatttgctaactggaggaaatgatgtactcattatttggcaaaattattacttatcatgctctttcactt

- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG