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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagatcacatatttgcaacgttttagcatgactacatttgctttctcgtttttatatattaaaatttggattctgcatttttcacaaaactaatcaacaaacttcaattactctgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACAGAAAGGCATGAGCAGAAGACCGGAGTGACGAAAGCTGAACATGTGACTG

Basic information

species Oryza sativa
transcript LOC_Os09g36220.2
intron # 3
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|58609928|gb|CK037961.1|CK037961
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|58605432|gb|CK033465.1|CK033465
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|33676452|gb|CF304691.1|CF304691
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|29670836|gb|CB667111.1|CB667111
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|33676098|gb|CF304337.1|CF304337
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|2428269|gb|C72732.1|C72732
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|58664572|gb|CK053258.1|CK053258
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|29638275|gb|CB643284.1|CB643284
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|58689405|gb|CK078092.1|CK078092
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|29679591|gb|CB675866.1|CB675866
EST:     TGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TACAGCGGTGTTCTTGATGTGCAGCATACTCAACGAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|29679636|gb|CB675911.1|CB675911
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|29634410|gb|CB639419.1|CB639419
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|33675681|gb|CF303920.1|CF303920
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|218502279|gb|FG970191.1|FG970191
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|157650573|gb|EX450207.1|EX450207
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|29625624|gb|CB630635.1|CB630635
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|29635476|gb|CB640485.1|CB640485
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
EST: gi|33676865|gb|CF305104.1|CF305104
EST:     GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTG                         TCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA
genomic: GGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACA

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: 70 (upstream exon), 66 (downstream exon)
Score: 115

TTTCAAATGCATGCTAAAGGGTGCTGCAGATTTCCTTGTTAAGCCAATACGGAAGAATGAATTAAGGAACTTATGGCAGCATGTTTGGAGAAAACAACTGgtaagatcac ... tgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACAGAAAGGCATGAGCAGAAGACCGGAGTGACGAAAGCTGAACATGTGACTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gattctgcatttttcacaaaactaatcaacaaacttcaattactctgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACAGAAAGGCATGAGCAGAAGACCGGAGTGACGAAAGCTGAACATGTGACTG
                   aactaat  putative branch site (score: 115)
                                          ctctgtttt  putative PPT
                 aaaactaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagatcacatatttgcaacgttttagcatgactacatttgctttctcgtttttatatattaaaatttggattctgcatttttcacaaaactaatcaacaaacttcaattactctgttttacagTCCAGCGGTGTTCTTGATGTGCAGCATACTCAACAAGAAGATAATCTTACAGAAAGGCATGAGCAGAAGACCGGAGTGACGAAAGCTGAACATGTGACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA