Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCAACCAACACATGCACAACTTAGAAGGGACTTAATGGAGCATATTTGGCAGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcacattgtcatgttcgttttcctgcaattatatcttacaatattttttctccctctacttttgttataaatttttgatatatttgtttttgtct...

Basic information

species Oryza sativa
transcript LOC_Os11g24590.1
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|88486237|gb|CI423508.1|CI423508
EST:     AGCGTTTTGGTCCATTTGCCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|86429327|gb|CI076008.1|CI076008
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|29633162|gb|CB638171.1|CB638171
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88281591|gb|CI402987.1|CI402987
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88517347|gb|CI445001.1|CI445001
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88511522|gb|CI439028.1|CI439028
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88846228|gb|CI372996.1|CI372996
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88476064|gb|CI413335.1|CI413335
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88284743|gb|CI406189.1|CI406189
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTNAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88508165|gb|CI435671.1|CI435671
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88282960|gb|CI404208.1|CI404208
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88488139|gb|CI425410.1|CI425410
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88483236|gb|CI420507.1|CI420507
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88510175|gb|CI437681.1|CI437681
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88834117|gb|CI077598.1|CI077598
EST:     AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: AGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
EST: gi|88271870|gb|CI387923.1|CI387923
EST:     GCGTTTTGGTCCATTTGGCAACAAGTAAAACAAATCAATCCTCCTGTATG                         GTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG
genomic: GCGTTTTGGTCCATTTGGCAACAAGTAAAACAA-TCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTG

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: 61 (upstream exon), 59 (downstream exon)
Score: 4

TCAACCAACACATGCACAACTTAGAAGGGACTTAATGGAGCATATTTGGCAGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcaca ... ttattttcagGTTATGTTAAAAGCCTAAGCACCTTTGAGGTTACTGTAAGCCAACATTTTGGAAAGCCAGAATCTCAAACAGTGTCCCGCTGGATTACTTGGGATATTGG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCAACCAACACATGCACAACTTAGAAGGGACTTAATGGAGCATATTTGGCAGCGTTTTGGTCCATTTGGCAACAAGTAAAACAATCAATCCTCCTGTATGgtgagtcacattgtcatgttcgttttcctgcaattatatcttacaatattttttctccctctacttttgttataaatttttgatatatttgtttttgtct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctccctc