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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttaagttacacagcttgctgttttcattattaatgttgattcacttgtatttttccatatcgcttccattttaagctgatgtgcttaagttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTACCATAGATTGCATGGTTATTTTTAGCAATGAAGCGTTTTGTCTACATAAA

Basic information

species Oryza sativa
transcript LOC_Os11g25980.1
intron # 1
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|88394093|gb|CI684763.1|CI684763
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88364266|gb|CI612215.1|CI612215
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGGATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAAGCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88396610|gb|CI601093.1|CI601093
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATAAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88463600|gb|CI696068.1|CI696068
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88592052|gb|CI710129.1|CI710129
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88313652|gb|CI671784.1|CI671784
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88589387|gb|CI707258.1|CI707258
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88760044|gb|CI769600.1|CI769600
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88578687|gb|CI687633.1|CI687633
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88453329|gb|CI565771.1|CI565771
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGGATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88761179|gb|CI770735.1|CI770735
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88591834|gb|CI709889.1|CI709889
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88388380|gb|CI683151.1|CI683151
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88342386|gb|CI645908.1|CI645908
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAANCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88410576|gb|CI686913.1|CI686913
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88576841|gb|CI673370.1|CI673370
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88419783|gb|CI686549.1|CI686549
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88578151|gb|CI674788.1|CI674788
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88729512|gb|CI753022.1|CI753022
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88589646|gb|CI708444.1|CI708444
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88590118|gb|CI708947.1|CI708947
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88581955|gb|CI699174.1|CI699174
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88591715|gb|CI709768.1|CI709768
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88763055|gb|CI772611.1|CI772611
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88391194|gb|CI595448.1|CI595448
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88581178|gb|CI698152.1|CI698152
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88335567|gb|CI642791.1|CI642791
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88579169|gb|CI688145.1|CI688145
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88349321|gb|CI678299.1|CI678299
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88458060|gb|CI695011.1|CI695011
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88344390|gb|CI677432.1|CI677432
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88381490|gb|CI682146.1|CI682146
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
EST: gi|88588861|gb|CI706703.1|CI706703
EST:     GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCG                         GACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC
genomic: GAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTAC

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), 73 (downstream exon)
Score: 7

TCTCCGTCTCCGCCGCCGCCTCCGCCTGCGCGGATCCCCATCCATCCCGCGAGCGAGCAGGGGCGCCGTCGTTCGTCCTGCCCTCTTCCGCCGCATCCCGgtgagcatcc ... ttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTACCATAGATTGCATGGTTATTTTTAGCAATGAAGCGTTTTGTCTACATAAA




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtatttttccatatcgcttccattttaagctgatgtgcttaagttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTACCATAGATTGCATGGTTATTTTTAGCAATGAAGCGTTTTGTCTACATAAA
                             agctgat  putative branch site (score: 7)
                                             ttttctgc  putative PPT
                                        ttaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cttaagttacacagcttgctgttttcattattaatgttgattcacttgtatttttccatatcgcttccattttaagctgatgtgcttaagttttctgcagGACTTATCAGTTTCAGTTAATCTCATGTGGGCAACCAGAGGGACAAATTACCATAGATTGCATGGTTATTTTTAGCAATGAAGCGTTTTGTCTACATAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - tgctgtt
- - - - - - - - - - - - - - - - - - -tgattca
- - - - - - - - - - - - - - - - - - - - - - cttgtat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgcttaa