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

...gcagctacccatgcgttgatgcgtgtgcatcggtcgcacgaatgccgcttgtttcttctgaccggtgagaaaattttgatggctctttttcattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGGCGTGCCTTACAACATGACACTTCTCAACTGCCTGCTATCTGCTTG

Basic information

species Oryza sativa
transcript LOC_Os01g65880.1
intron # 2
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|88299745|gb|CI577247.1|CI577247
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88299494|gb|CI574607.1|CI574607
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|117218417|gb|CT858164.1|CT858164
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88571732|gb|CI663105.1|CI663105
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         CGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88337815|gb|CI632317.1|CI632317
EST:     GCAATGTCATCGCTCTCTTCCTGTTCNTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATTAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58671599|gb|CK060285.1|CK060285
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88372296|gb|CI619626.1|CI619626
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|55827951|gb|AU064019.2|AU064019
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58686371|gb|CK075058.1|CK075058
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88338521|gb|CI645775.1|CI645775
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|4715911|gb|AU057027.1|AU057027
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58596407|gb|CK006935.1|CK006935
EST:     GCAATGTCATCGCTCTCTTCCGGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88313297|gb|CI594927.1|CI594927
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58663811|gb|CK052497.1|CK052497
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88453324|gb|CI565766.1|CI565766
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88574722|gb|CI666491.1|CI666491
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|12622713|gb|AU172926.1|AU172926
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58675409|gb|CK064096.1|CK064096
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58595504|gb|CK006032.1|CK006032
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58666605|gb|CK055291.1|CK055291
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|4880424|gb|AU064723.1|AU064723
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTNCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58596723|gb|CK007251.1|CK007251
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCGTCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58687982|gb|CK076669.1|CK076669
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|8856858|gb|AU094176.1|AU094176
EST:     CAATGTCATCGCTTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGNAGGATCATCAAGAAGAGATCAACGNAGGACTTCTCCGG
genomic: CAATGTCATCGC-TCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|4880538|gb|AU064837.1|AU064837
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCANCAAGAAGAGATCANCGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58598047|gb|CK008575.1|CK008575
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58590655|gb|CF988963.1|CF988963
EST:     GCAATGTCATCGGTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88406334|gb|CI596461.1|CI596461
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58669012|gb|CK057698.1|CK057698
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88340153|gb|CI650600.1|CI650600
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|25797892|gb|CA753853.1|CA753853
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58601031|gb|CK011559.1|CK011559
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88431567|gb|CI579684.1|CI579684
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88354075|gb|CI636273.1|CI636273
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGANTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58597601|gb|CK008129.1|CK008129
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|58590858|gb|CF989166.1|CF989166
EST:     GCAATGTCATCGCTCTCTTCCTGTTGCGTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTT-CCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88375222|gb|CI680981.1|CI680981
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|29684974|gb|CB681249.1|CB681249
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCGGCGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|29658996|gb|CB655271.1|CB655271
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88577893|gb|CI674506.1|CI674506
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
EST: gi|88569829|gb|CI661004.1|CI661004
EST:     GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGT                         TGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG
genomic: GCAATGTCATCGCTCTCTTCCTGTTCCTTTCGCCAGTgtaagtttct ... cattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgcttgtttcttctgaccggtgagaaaattttgatggctctttttcattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGGCGTGCCTTACAACATGACACTTCTCAACTGCCTGCTATCTGCTTG
                                     ctctttttcattttac  CT-rich tract
                                      tctttttcatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcagctacccatgcgttgatgcgtgtgcatcggtcgcacgaatgccgcttgtttcttctgaccggtgagaaaattttgatggctctttttcattttacagTGTCACCTTCTGGAGGATCATCAAGAAGAGATCAACGGAGGACTTCTCCGGCGTGCCTTACAACATGACACTTCTCAACTGCCTGCTATCTGCTTG

gcagcta
- - - -cccatgc
- - - - - - - gttgatg
- - - - - - - - - - - - gtgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgatgg