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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cagtataccactagttgtaactcatactagcagaggatttttggcttgaagttgtggctttctccaaggctgatctacaacttgggttcgctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGCTGCAGCGCGCACACCGGGGAGGGCCTTCTTCAAGGTTTCGATTGGCTCG

Basic information

species Oryza sativa
transcript LOC_Os02g22140.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g22140.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G154890_T03 (Zea mays), 3'ss of exon 5
cagtataccactagttgtaactcatacta-gcagaggatttttggcttgaagttgtggctttctccaaggctgatctac--aacttgggttcgctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGCTGCAGCGCGCACACCGGGGAGGGCCTTCTTCAAGGTTTCGATTGGCTCG
 | | |     |  |   ||  || | |  ||||       |  |  | |  || |||| || |||| ||| |  | ||  | |||   |   || ||||||||| || ||| |||||| ||||||| ||||| |||||||| |||| || |||||||||||  |||| || ||||| |||||  | || ||||| ||||| |
tattttgtttgtgctgcgaatgcagaatctgcagttccccatctgaattagtttatggccttttccacggcaggccgactcaccttccat---cttttttcagGTTCTGAATCTGGAAGTGATGGACAGAAGCAGGCACTGGAAGATTGTGGGCTGCAGCGCTTACACGGGAGAGGGGCTTCTCGAGGGCTTCGACTGGCTGG
















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|88508846|gb|CI436352.1|CI436352
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|87011505|gb|CI279414.1|CI279414
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88512554|gb|CI440060.1|CI440060
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88508615|gb|CI436121.1|CI436121
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86254838|gb|CI061149.1|CI061149
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|218480621|gb|FG956869.1|FG956869
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86855702|gb|CI269029.1|CI269029
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88837858|gb|CI371436.1|CI371436
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86426604|gb|CI071701.1|CI071701
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88539638|gb|CI469611.1|CI469611
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88471435|gb|CI408706.1|CI408706
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCATAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88474719|gb|CI411990.1|CI411990
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88850497|gb|CI093178.1|CI093178
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88489176|gb|CI426448.1|CI426448
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86836752|gb|CI347369.1|CI347369
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86839729|gb|CI343657.1|CI343657
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88447174|gb|CI531417.1|CI531417
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88442202|gb|CI560443.1|CI560443
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86428862|gb|CI075543.1|CI075543
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86483236|gb|CI125869.1|CI125869
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88491910|gb|CI429182.1|CI429182
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTNAAATTGNTAAG                         TAACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88291619|gb|CI537405.1|CI537405
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86487786|gb|CI130419.1|CI130419
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88531376|gb|CI459846.1|CI459846
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88560491|gb|CI491160.1|CI491160
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88224286|gb|CI224135.1|CI224135
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88552166|gb|CI482295.1|CI482295
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86489199|gb|CI131832.1|CI131832
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88551962|gb|CI482063.1|CI482063
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88488976|gb|CI426247.1|CI426247
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88961256|gb|CI096660.1|CI096660
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|15857754|gb|BI810566.1|BI810566
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTAAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|86500170|gb|CI142803.1|CI142803
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88483388|gb|CI420659.1|CI420659
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
EST: gi|88551702|gb|CI481782.1|CI481782
EST:     CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAG                         GTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC
genomic: CAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGC

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: 51 (upstream exon), 44 (downstream exon)
Score: 9

AGACTAGCAGGAGCTTCATTGCTGGTGTTTGCAAATAAGCAAGATATTCAAGGCGCTCTCAAACCTTCTGAAATTGCTAAGgtaagcagat ... ctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGCTGCAGCGCGCACACCGGGGAGGGCCTTCTTCAAGGTTTCGATTGGCTCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgaagttgtggctttctccaaggctgatctacaacttgggttcgctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGCTGCAGCGCGCACACCGGGGAGGGCCTTCTTCAAGGTTTCGATTGGCTCG
                      ggctgat  putative branch site (score: 9)
                                             ctgttttc  putative PPT
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cagtataccactagttgtaactcatactagcagaggatttttggcttgaagttgtggctttctccaaggctgatctacaacttgggttcgctgttttcagGTACTCAATTTGGAAGCGATGGACGGAAGCCGGCACTGGCAGATCGTAGGCTGCAGCGCGCACACCGGGGAGGGCCTTCTTCAAGGTTTCGATTGGCTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - -gcttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggctgat