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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaattattcattggtcgtagtagtctttcgtcagaagatatatatctgtacataacccaatatcttcctcatcagagacagtcgttgcaaactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGAGGTTGCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGC

Basic information

species Oryza sativa
transcript LOC_Os01g04950.1
intron # 1
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|58669344|gb|CK058030.1|CK058030
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAG--TGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88358200|gb|CI605125.1|CI605125
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|58670561|gb|CK059247.1|CK059247
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAG--TGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88762509|gb|CI772065.1|CI772065
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88414987|gb|CI601819.1|CI601819
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|29646409|gb|CB651416.1|CB651416
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88336924|gb|CI627004.1|CI627004
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88431719|gb|CI576910.1|CI576910
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88745560|gb|CI768920.1|CI768920
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|117229908|gb|CT846338.1|CT846338
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGT--GAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88363891|gb|CI607201.1|CI607201
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88726212|gb|CI749867.1|CI749867
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88316937|gb|CI625574.1|CI625574
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88395178|gb|CI609494.1|CI609494
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTTAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88354396|gb|CI624786.1|CI624786
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGC-ACTGTGAGAGTGTGAGCTGAGGTGAGCATCGGCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88402788|gb|CI613236.1|CI613236
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88370557|gb|CI590135.1|CI590135
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88739283|gb|CI762791.1|CI762791
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|58609810|gb|CK037843.1|CK037843
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCGG                         GTAGCCAGCCACTGT--GAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88736884|gb|CI760392.1|CI760392
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88723934|gb|CI745631.1|CI745631
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88736975|gb|CI760483.1|CI760483
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|88763877|gb|CI773293.1|CI773293
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|58673495|gb|CK062181.1|CK062181
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGTGAGT-TGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|58673905|gb|CK062591.1|CK062591
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGT--GAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
EST: gi|58693491|gb|CK082178.1|CK082178
EST:     CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAG                         GTAGCCAGCCACTGT--GAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA
genomic: CTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGA

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: 65 (upstream exon), 71 (downstream exon)
Score: 5

ATGTCTTCTTCTTCAGCTCGGTCTTGGTTGCCGACCTCATTTGCAGATTTCTGCACATGAGGCATCTCTCTCTCGAAGTATCGTGTTTTGATTTGGGCAGgtatgagcaa ... aactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGAGGTTGCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgtacataacccaatatcttcctcatcagagacagtcgttgcaaactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGAGGTTGCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGC
     acataac  putative branch site (score: 5)
              aatatctt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaattattcattggtcgtagtagtctttcgtcagaagatatatatctgtacataacccaatatcttcctcatcagagacagtcgttgcaaactttgcagGTAGCCAGCCACTGTGAGAGTGTGAGCTGAGGTGAGCATCGCCATGGGAGAGGTTGCAGAAGACATCTACACCCAAGATGGCACCGTGGACGTCAAGGGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - ctgtaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - aacccaa