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'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaaacatcgcaaaaaaacagtgtggatctttatgattcattggttttccaatgtggaatggcctcatgctgatttctgtcacctgctgaatgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATCTATGGAAATGAGCCCATCATGTCGGTTGCTGATATGAAAGATGTCCTTG

Basic information

species Oryza sativa
transcript LOC_Os03g42750.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 24
lower sequence: GRMZM2G099056_T01 (Zea mays), 3'ss of exon 24
------------gcaaacatcgcaaaaaaacagtgtggatctttatgattcattggttttccaatgtggaatggcc---tcatgctgatttctgtcacctgct-gaatgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATCTATGGAAATGAGCCCATCATGTCGGTTGCTGATATGAAAGATGTCCTTG
             | | | |   |  |  |  || ||| ||  |||    |   ||  |       ||  | |  |   | | ||||||| || | | |||||  ||   |||||||| |||||||||||||| ||||||||||| ||||||||||| || ||||| ||||| |||||||| |||||||| ||    || |||||||| |||||||
gttagccactcgaccatcctattattatgaatgtttggttcactattgcccccaggagtcattgcttgagacgttccacttaagctgattgct-taatctgctcaaacacttgcagAAGGAGTTTTTGGACAAATACGAGAGCTTTGTTCAGATGGTAACACGGATATATGGGAATGAGCCGATCATGTCAGTCAACGAAATGAAAGACGTCCTTG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 24
lower sequence: AT1G47550.1 (Arabidopsis thaliana), 3'ss of exon 24
------gcaaacatcgcaaaa--aaacagtgtggatctttatgattcattggttttccaatgtggaatggcctcatgctgatttctgtcacctgctgaatgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATCTATGGAAATGAGCCCATCATGTCGGTTGCTGATATGAAAGATGTCCTTG
      |   | |  | |||    || || ||      | |   | ||||  |    || |||    ||     ||||    || ||| ||||  | ||      ||||| |||||| |||||||||||||||||||||| ||| | ||  |     | |||   | |||   | |       ||  |||| |||| ||   | || |
gtaccagtttaaactgaaaagttgaagagagtaataaataacagtgcattattagctcagtgtt---tgaatcaatgcgttgttgtgtgacct--taaa------cagAAGGAGTTTCTGGACAAGTACGAGAGCTTCGTGCAGCTCGTAGCCAAAGTTTATCCGAGTGAAAACGTTCCTGGAGTAACTGAAATGAGAGGACTTCTGG

upper sequence: LOC_Os03g42750.1 (Oryza sativa), 3'ss of exon 24
lower sequence: AT1G47560.1 (Arabidopsis thaliana), 3'ss of exon 24
gcaaacatcgcaaaaaaacagt-gtggatctttatgattcattggttttccaatgtggaatggcctcatgctgatttctgtcacctgctgaatgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATCTATGGAAATGAGCCCATCATGTCGGTTGCTGATATGAAAGATGTCCTTG
| |  |||   ||   || ||| | |||   | || | | |  |    | || | |    |       ||      |  ||       |||   |   ||||| |||||| |||||||||||||||||||||| ||| | ||  |     | ||    | |||   | |      |||  |||| |||| ||   | || |
gtacccatttaaactgaaaagttgaggagagtaataaataacag----tgcattattagctcagtgtttgaatcaatgcgttgttgtgtgaccttaaacagAAGGAGTTTCTGGACAAGTACGAGAGCTTCGTGCAGCTCGTAGCCAAAGTTTACCCGAGTGAAAACGTTCCTGGGGTAACTGAAATGAGAGGACTTCTGG

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|29667112|gb|CB663387.1|CB663387
EST:     AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAG                         AAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
genomic: AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAGgtaagctagc ... atgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
EST: gi|29656592|gb|CB652867.1|CB652867
EST:     AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAG                         AAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
genomic: AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAGgtaagctagc ... atgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
EST: gi|29657699|gb|CB653974.1|CB653974
EST:     AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAG                         AAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
genomic: AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAGgtaagctagc ... atgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
EST: gi|29639555|gb|CB644564.1|CB644564
EST:     AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAG                         AAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
genomic: AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAGgtaagctagc ... atgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
EST: gi|38477138|gb|CF961271.1|CF961271
EST:     AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAG                         AAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
genomic: AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAGgtaagctagc ... atgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
EST: gi|29676302|gb|CB672577.1|CB672577
EST:     AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAG                         AAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
genomic: AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAGgtaagctagc ... atgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
EST: gi|29645304|gb|CB650311.1|CB650311
EST:     AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAG                         AAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC
genomic: AGACACTGACTTCTGATGAGTTGTTTCCTTCACTGTGGGACAAGTGCAAGgtaagctagc ... atgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttccaatgtggaatggcctcatgctgatttctgtcacctgctgaatgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATCTATGGAAATGAGCCCATCATGTCGGTTGCTGATATGAAAGATGTCCTTG
                      tgctgat  putative branch site (score: 3)
                                            aatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaaacatcgcaaaaaaacagtgtggatctttatgattcattggttttccaatgtggaatggcctcatgctgatttctgtcacctgctgaatgtttgcagAAAGAGTTTTTGGACAAGTACGAGAGCTTCGTTCAGATGGTGACGCGGATCTATGGAAATGAGCCCATCATGTCGGTTGCTGATATGAAAGATGTCCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
gcaaaca
- - - - - caaaaaa
- - - - - - - - - - - gtggatc
- - - - - - - - - - - - - - - - -tgattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - tggaatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cctgctg