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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatcttctgcttgattcacaataaccatatatggactgagtctagcttgtaagtagcctagtattgatattgttgaactactcacactttgtaagtttttcttttaaaaatgcag

Basic information

species Oryza sativa
transcript LOC_Os01g51380.1
intron # 2
splice site 5'
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|88352648|gb|CI624587.1|CI624587
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88724403|gb|CI747662.1|CI747662
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88433134|gb|CI569803.1|CI569803
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|58672899|gb|CK061585.1|CK061585
EST:     GCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGCAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: GCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTG-AGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88358211|gb|CI605136.1|CI605136
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88360936|gb|CI625242.1|CI625242
EST:     TGCAAATGGTAATGTCGAAACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|163927702|gb|EG710506.1|EG710506
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88317359|gb|CI628008.1|CI628008
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88345261|gb|CI627902.1|CI627902
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88397163|gb|CI593375.1|CI593375
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88371072|gb|CI597549.1|CI597549
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88360978|gb|CI625284.1|CI625284
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|86901596|gb|CI310358.1|CI310358
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88356589|gb|CI626204.1|CI626204
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88724311|gb|CI747570.1|CI747570
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88314360|gb|CI604844.1|CI604844
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|88388263|gb|CI627802.1|CI627802
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
EST: gi|66915737|gb|CX102585.1|CX102585
EST:     TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGG                         AGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG
genomic: TGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatct ... aaaaatgcagAGTACAGGACAGTCTCTGGAGTTGCTGGTCCTCTAGTCATTCTTGATAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGGCTTCTTCTACAATCTCAAACATGGTTGTTGCAAATGGTAATGTCGACACGGAGGAAGGAACTCTTGAGATTGGGATGGgtacggatcttctgcttgattcacaataaccatatatggactgagtctagcttgtaagtagcctagtattgatattgttgaactactcacactttgtaagtttttcttttaaaaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA