Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcggaggcttgcaaatatttttgttgctgaacatcagtttccgttctgagttcatatcgttgatcaataacatcgttaacacctatttcttgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCAAAACAGTACTCCAGCCAACATGAATCAGCTCGAGCGTTGAGGCTTTGCC

Basic information

species Oryza sativa
transcript LOC_Os01g11590.2
intron # 8
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|86495872|gb|CI138505.1|CI138505
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88285948|gb|CI512605.1|CI512605
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|86503409|gb|CI146042.1|CI146042
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|86493851|gb|CI136484.1|CI136484
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|86504299|gb|CI146932.1|CI146932
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88418714|gb|CI506475.1|CI506475
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|29685008|gb|CB681283.1|CB681283
EST:     TCAAGCTTGAATGGCTAGTATCTCACGCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: TCAAGCTTGAATGGCTAG-ATCTCAC-CTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|87019245|gb|CI279755.1|CI279755
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88292773|gb|CI505352.1|CI505352
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88303568|gb|CI508174.1|CI508174
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88418742|gb|CI506503.1|CI506503
EST:     ATTCAAGCTTGAATGGCTAGATGTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88563670|gb|CI494387.1|CI494387
EST:     ATTCAAGCTTGAATGGGTAGATCTCACCTGAAGAAAAAAGAGGATTGGAG                         CTTTGCCAAATTGCTGCACGATAANTGAAGCGCCAACCATTGGGACAACCG
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88563238|gb|CI493955.1|CI493955
EST:     AAAAA-AGAATT-GAGG                         CTTTGCCNAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACC
genomic: AAAAAGAGAATTGGA-Ggtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACC
EST: gi|88462351|gb|CI512016.1|CI512016
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTNCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88464783|gb|CI512088.1|CI512088
EST:     ATTCAAGCTTGAATGGGTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|29663498|gb|CB659773.1|CB659773
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88257898|gb|CI360484.1|CI360484
EST:     ATTCAAGCTTG-ATGGCTATATCTCACCTGAAGGAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88567451|gb|CI498168.1|CI498168
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTTAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88567515|gb|CI498232.1|CI498232
EST:     ATTCAAGCTTGAATTGCTAGATCTCACCTGAAGAAGAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|88567495|gb|CI498212.1|CI498212
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         G
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcag-
EST: gi|88567495|gb|CI498212.1|CI498212
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         G
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcag-
EST: gi|88438085|gb|CI536244.1|CI536244
EST:     TTCAAGGCTTGAATGGGTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: TTCAA-GCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
EST: gi|29663497|gb|CB659772.1|CB659772
EST:     ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAG                         CTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA
genomic: ATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCA

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), 71 (downstream exon)
Score: 14

ATTAGCTTGTATAGTTGAGATGGAAAAGGAGAATTCAAGCTTGAATGGCTAGATCTCACCTGAAGAAAAAAGAGAATTGGAGgtactttact ... tgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCAAAACAGTACTCCAGCCAACATGAATCAGCTCGAGCGTTGAGGCTTTGCC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgagttcatatcgttgatcaataacatcgttaacacctatttcttgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCAAAACAGTACTCCAGCCAACATGAATCAGCTCGAGCGTTGAGGCTTTGCC
                                    cctatttctt  CT-rich tract
                                      tatttcttgaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcggaggcttgcaaatatttttgttgctgaacatcagtttccgttctgagttcatatcgttgatcaataacatcgttaacacctatttcttgaatatcagCTTTGCCAAATTGCTGCACGATAAGTGAAGCGCCAACCATTGGGACAACCAAAACAGTACTCCAGCCAACATGAATCAGCTCGAGCGTTGAGGCTTTGCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - gcttgca
- - - - - - - - - - -tgttgct
- - - - - - - - - - - - - - -aacatca
- - - - - - - - - - - - - - - - - - - - -cgttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aataaca