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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtactgccatcatcattttattgaggctgcaaaatgaaatttatctgacattattcataagccactgcagtaacatttggctgaattaaattgtttctccctgtatctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGACACACCTTCTGAGGGCTCGGGAGAAGGGCAAACCACAGATGAATAGCTTC

Basic information

species Oryza sativa
transcript LOC_Os03g20100.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g20100.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM5G862107_T01 (Zea mays), 3'ss of exon 6
gtactgccatcatcattttattgaggctgcaaaatgaaatt-tatctgacatta-ttcataagccactgcagtaacatttggctgaattaa---attgtttctcc--ctgtatctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGACACACCTTCTGAGGGCTCGGGAGAAGGGCAAACCACAGATGAATAGCTTC------
||| ||| | | |    || || | ||| |    | ||||   || | |  | | ||||   |    || |  | ||| |||||||  |||   | |  | ||||  ||||| |||||||||||||||||| || ||||||||||||||||||||||| ||||| || || ||  ||||||| ||||  || | |||  |      |||||||||||||   |      
gtattgcaaacgttcccttgttaatgctaccgtgtcaaatcacatttcatctaacttcaactgtgtgtgtaa-atcatgtggctgagctaatcgaatcatcctcctgctgtacctcttcacagAGTGGATTGACCCTCAGTTCAGAGGGCATCTTAGGACCATTGTCGTCGGATGCACCTTCGGAGGATTCTGAAGATCG------CACAGATGAATAGAGGCAGTTGA
















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|14713903|gb|AU197855.1|AU197855
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88516254|gb|CI443908.1|CI443908
EST:     TCAAGCAGAGGCAATGGCTCGTGGCTGATATGTTAAGATTCCACCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: TCAAGCAGAGGCAATGGCTCGT-GCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|86546307|gb|CI186513.1|CI186513
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|86866733|gb|CI343547.1|CI343547
EST:     CTCAAGCAGAGGCAATGGCTC-TGCTGATAT-TTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88974484|gb|CI022025.1|CI022025
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88512903|gb|CI440409.1|CI440409
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTGTCAGTTCATAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88975584|gb|CI021666.1|CI021666
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|18388863|gb|BM422061.1|BM422061
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|218483682|gb|FG943816.1|FG943816
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88983198|gb|CI020762.1|CI020762
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88219484|gb|CI219044.1|CI219044
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88284294|gb|CI405740.1|CI405740
EST:     TCAAGCAGAGGCAATGGGCTCGTGCTGATATNTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: TCAAGCAGAGGCAAT-GGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|29638067|gb|CB643076.1|CB643076
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88277167|gb|CI397969.1|CI397969
EST:     TATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: TATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88218693|gb|CI218542.1|CI218542
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         ATTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|13165466|gb|AU174263.1|AU174263
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATNTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|29662710|gb|CB658985.1|CB658985
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|29660922|gb|CB657197.1|CB657197
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|29645770|gb|CB650777.1|CB650777
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|86853874|gb|CI329320.1|CI329320
EST:     CTCAAGCAGAGGCAATGGATCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGA-GGCATGTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|87010736|gb|CI312428.1|CI312428
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|88516966|gb|CI444552.1|CI444552
EST:     CTCAAGCAGAGGCAATTGCTCGTNCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGNCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|29660751|gb|CB657026.1|CB657026
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|3768542|gb|AU032569.1|AU032569
EST:     TCAAGTCNGAGGCNATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCNTCTTAGGGCCATTATCATCAGAC
genomic: TCAAG-CAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
EST: gi|29638932|gb|CB643941.1|CB643941
EST:     CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAG                         AGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC
genomic: CTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGAC

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: 64 (upstream exon), 69 (downstream exon)
Score: 41

GCTGATGAGATGGCTCAGATATTCAGGCAGAGGATAGCTCAAGCAGAGGCAATGGCTCGTGCTGATATGTTAAGATTCCAGCCTGAGgtactgccat ... ctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGACACACCTTCTGAGGGCTCGGGAGAAGGGCAAACCACAGATGAATAGCTTC




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccactgcagtaacatttggctgaattaaattgtttctccctgtatctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGACACACCTTCTGAGGGCTCGGGAGAAGGGCAAACCACAGATGAATAGCTTC
      cagtaac  putative branch site (score: 41)
                             ttgtttctccctgtat  putative PPT
                    tgaattaaattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtactgccatcatcattttattgaggctgcaaaatgaaatttatctgacattattcataagccactgcagtaacatttggctgaattaaattgtttctccctgtatctcttcacagAGTGGATTAACTCTCAGTTCAGAGGGCATCTTAGGGCCATTATCATCAGACACACCTTCTGAGGGCTCGGGAGAAGGGCAAACCACAGATGAATAGCTTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG