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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatagtagttctataattgaatatatttatcagagtaagaagtaaactgggcatgagaaaagtgtttatcattttaattgcttatcttgatttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCGGTGCGTGCGTTAGTTTTACTCGCCTCAGGGACAACATGGGCGAGGATCA

Basic information

species Oryza sativa
transcript LOC_Os01g13770.2
intron # 10
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|88988962|gb|CI040692.1|CI040692
EST:     GATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGATGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88963076|gb|CI026750.1|CI026750
EST:     AGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: AGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|89173009|gb|CI040902.1|CI040902
EST:     GGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88215807|gb|CI215656.1|CI215656
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86418717|gb|CI053518.1|CI053518
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|29640948|gb|CB645955.1|CB645955
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86528722|gb|CI168928.1|CI168928
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88972974|gb|CI019593.1|CI019593
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88214268|gb|CI214117.1|CI214117
EST:     GTGTTGCNATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88474229|gb|CI411500.1|CI411500
EST:     ATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: ATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86505322|gb|CI147955.1|CI147955
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88383671|gb|CI545822.1|CI545822
EST:     TACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: TACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|7652120|gb|AU089726.1|AU089726
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88980311|gb|CI026578.1|CI026578
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88975808|gb|CI024059.1|CI024059
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86506827|gb|CI149460.1|CI149460
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|87012744|gb|CI295188.1|CI295188
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|89169034|gb|CI020574.1|CI020574
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88971539|gb|CI017853.1|CI017853
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86840531|gb|CI333826.1|CI333826
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAAATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86874333|gb|CI335945.1|CI335945
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88214214|gb|CI214063.1|CI214063
EST:     GTGTTGCTATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88988160|gb|CI036130.1|CI036130
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86522230|gb|CI162436.1|CI162436
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|33797638|gb|CF324678.1|CF324678
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|700666|gb|D46957.1|D46957
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88219350|gb|CI218910.1|CI218910
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|55409685|gb|CV722061.1|CV722061
EST:     GAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86525001|gb|CI165207.1|CI165207
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|10794973|gb|AU108939.1|AU108939
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGANGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|89171895|gb|CI040405.1|CI040405
EST:     AAGATCGAAGAGGAGAAAAGG                         TCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCTAGGTGGCTGCG
genomic: AAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88979266|gb|CI025768.1|CI025768
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88225172|gb|CI225088.1|CI225088
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|88465192|gb|CI517361.1|CI517361
EST:     TACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGC-
genomic: TACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|86250673|gb|CI003791.1|CI003791
EST:     GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
EST: gi|89194311|gb|CI116748.1|CI116748
EST:     GTGTTGCCATCTACTCGTACATCGAGGCTAAGATCGAAGAGGAGAAAAGG                         GCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG
genomic: GTGTTGCCATCTACTCGTACATCAAGGCTAAGATCGAAGAGGAGAAAAGGgtaagttcat ... tttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgggcatgagaaaagtgtttatcattttaattgcttatcttgatttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCGGTGCGTGCGTTAGTTTTACTCGCCTCAGGGACAACATGGGCGAGGATCA
            aaaagtgtttatcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatagtagttctataattgaatatatttatcagagtaagaagtaaactgggcatgagaaaagtgtttatcattttaattgcttatcttgatttggtacagGCGAAGAGTGCATGATGAGGTGGTTTCTGTGAATATGGCAAGGTGGCTGCGGTGCGTGCGTTAGTTTTACTCGCCTCAGGGACAACATGGGCGAGGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT