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

...agaaccttttatgttagctctgaaaggtttattgttccatgcagattgctattcctttaactatatgattaacaccttttgtccttttgttgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGAGCTTCCTCTGGCGAAGAAAGCCACCAGGACATCTCAATCACCTCGGTTA

Basic information

species Oryza sativa
transcript LOC_Os02g31290.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 14
lower sequence: GRMZM5G814700_T01 (Zea mays), 3'ss of exon 4
agaaccttttatgttagctctgaaaggtttattgttccatgcagattgctattcctttaactatatgattaacaccttttgtccttttgttgt-----ccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGAGCTTCCTCTGGCGAAGAAAGCCACCAGGACATCTCAATCACCTCGGTTA
|    ||  |   | |  || |||     | |  ||   |||    |||  | | |||||  ||||| ||   |  ||||| | |||||| ||        | ||||||| ||||| |||||| ||||||||||||||||||| |||||||| ||  |||| || || |||||||  ||||| ||||||   |    || |   |
aatgtctgcttaataatttcagaacttgctctatttttgtgc---ctgcagtgcttttaagcatatggttgcaa--ttttgacattttgtcgtgatctttctcagGAACCTTTCCCCATGGGTTCAAACATCCGAGCCAGGTCTGGGAGATCCCGGACTTCTTCGGGTGAAGAAAATCACCATGACATCCAGACAGTCTTGACCA
















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|58687890|gb|CK076577.1|CK076577
EST:     GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAG                         GAACCATTCCCTATGGGTACAAACATC
genomic: GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctt ... tgtccattagGAACCATTCCCTATGGGTACAAACATC
EST: gi|24208728|gb|AU225755.1|AU225755
EST:     GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAG                         GAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
genomic: GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctt ... tgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
EST: gi|58691922|gb|CK080609.1|CK080609
EST:     GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAG                         GAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
genomic: GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctt ... tgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
EST: gi|58657140|gb|CK045820.1|CK045820
EST:     GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAG                         GAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
genomic: GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctt ... tgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
EST: gi|4969156|gb|AU066060.1|AU066060
EST:     GCTGCCGNCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAG                         GAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
genomic: GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctt ... tgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
EST: gi|58696242|gb|CK084929.1|CK084929
EST:     GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAG                         GAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
genomic: GCTGCCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctt ... tgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
EST: gi|88840701|gb|CI080155.1|CI080155
EST:     CCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAG                         GAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA
genomic: CCGCCCCATACTATTCCATTCGGATGGTCCTAATGCAGGAGATCAGgtatgatctt ... tgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgctattcctttaactatatgattaacaccttttgtccttttgttgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGAGCTTCCTCTGGCGAAGAAAGCCACCAGGACATCTCAATCACCTCGGTTA
                     gattaac  putative branch site (score: 2)
                             ccttttgtccttttgt  CT-rich tract
          tttaactatatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaaccttttatgttagctctgaaaggtttattgttccatgcagattgctattcctttaactatatgattaacaccttttgtccttttgttgtccattagGAACCATTCCCTATGGGTACAAACATCCGAGCCAGGTCAGGGAGATCGCGAGCTTCCTCTGGCGAAGAAAGCCACCAGGACATCTCAATCACCTCGGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - ttatgtt
- - - - - - - - - - - - - - - - - -tccatgc
- - - - - - - - - - - - - - - - - - - - - - - tgctatt