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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagaatacggtttgtttgagtgtcatctggcacaatattgttttacactatgatgagttggagatttggttacctagtaaagtcgatgaatcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAAGGTGGTTTTGGACAGGTTTATGTTGGCAGAAGGGTTTCTGGTGGAACTG

Basic information

species Oryza sativa
transcript LOC_Os01g56580.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G116086_T01 (Zea mays), 3'ss of exon 2
tagaatacggtttgtttgagtgtcatctggcacaatattgttttacactatgat--gagttggagatttggttacctagtaaagtcgatgaatcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAAGGTGGTTTTGGACAGGTTTATGTTGGCAGAAGGGTTTCTGGTGGAACTG
||    || | |      | ||    |     | | |   |   |   ||| |   || ||| | ||||||| ||||  ||||    |    || ||||||||||||||||||||||||||| || |||||||| || || ||||||||||||||||||||||| || || ||||||||||||||| ||||||| ||||| |
taactgacagctctagccaatggtgccaaaagctagaac-tgcaaatgtataactggatttgaaaatttggtcacctt-taaatgataaatttcttttgcagGTTCAAGTAGGCCATTCTCCACAGTACAAGGTTGAACGCAAGTTGGGGAAAGGTGGTTTTGGGCAAGTATATGTTGGCAGAAGGATTTCTGGGGGAACAG

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT3G03940.1 (Arabidopsis thaliana), 3'ss of exon 2
tagaatacggtttgtttga--gtgtcatctggcacaa-tattgttttacactatgatgagttggagatttggttacctagtaaagtcgatgaatcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAAGGTGGTTTTGGACAGGTTTATGTTGGCAGAAGGGTTTCTGGTGGAACTG
   |||  ||||||   |    || ||   ||   ||   |||   ||   | |  |        ||    | ||   | ||   |    |  |  | |  |||| ||||| ||  |||||||    || |||   ||| ||||  | || |||||||| ||||| || ||||||||||||||||||||   |||||| | ||
--aaatgtggtttgcgaggccatgccaatgggtttaagccttgcactagctttttgttctcctttgagagagatattcactatgattt-cgttttctgtatagGTACAAGTTGGAAATTCTCCTGTTTATAAGACGGAGAGGAAACTTGGTAAAGGTGGCTTTGGTCAAGTTTATGTTGGCAGAAGGGTGAGTGGTGGCAGTG

upper sequence: LOC_Os01g56580.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv08s0007g07420.t01 (Vitis vinifera), 3'ss of exon 2
tagaatacggtttgtttgagtgtcatctggcacaatattgttttacactatgatgagttggagatttggtta-----cctagtaaagtcgatgaatcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAAGGTGGTTTTGGACAGGTTTATGTTGGCAGAAGGGTTTCTGGTGGAACTG
     |  |    | |   |   ||| ||  | ||| ||   ||      |  |        ||||   | |      |||||    |       |   ||  |||| ||||| ||  |||||||   ||||||| ||||  ||||||| || || ||||||||||| || || |||||||||||||||||   |||||| ||||
-----tctgaggggctaatggagcatttgttaaaatttttccttcactcgttcttcaacacggattctttcaaagcatctagttgttttctgtttttggttctagGTACAAGTGGGTAATTCTCCTATATACAAGATAGAAAGGAAGTTAGGTAAGGGTGGTTTTGGTCAAGTGTATGTTGGCAGAAGGGTAAGTGGTGGCACTG

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|29629024|gb|CB634035.1|CB634035
EST:     AGATTGGTGGAGGTGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAG                         GTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA
genomic: AGATTGGTGGAGGCGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAGgtatattctt ... tcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA
EST: gi|88720002|gb|CI745301.1|CI745301
EST:     AGATTGGTGGAGGCGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAG                         GTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA
genomic: AGATTGGTGGAGGCGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAGgtatattctt ... tcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA
EST: gi|29623307|gb|CB628318.1|CB628318
EST:     AGATTGGTGGAGGTGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAG                         GTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA
genomic: AGATTGGTGGAGGCGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAGgtatattctt ... tcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA
EST: gi|58661787|gb|CK050467.1|CK050467
EST:     AGATTGGTGGAGGTGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAG                         GTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA
genomic: AGATTGGTGGAGGCGAAGATGATGGGAATGCATCTCCAGTTCCGGATAAGgtatattctt ... tcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactatgatgagttggagatttggttacctagtaaagtcgatgaatcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAAGGTGGTTTTGGACAGGTTTATGTTGGCAGAAGGGTTTCTGGTGGAACTG
                                           aatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagaatacggtttgtttgagtgtcatctggcacaatattgttttacactatgatgagttggagatttggttacctagtaaagtcgatgaatcatttgcagGTTCAAGTAGGCCATTCTCCGCAATACAAGGTAGAGCGGAAGTTGGGGAAAGGTGGTTTTGGACAGGTTTATGTTGGCAGAAGGGTTTCTGGTGGAACTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA