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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatgttgctttcaggattacaaattatcatggtttttaatgttctttctaattcctacttttgctgtttggatgggaatag

Basic information

species Oryza sativa
transcript LOC_Os03g63430.1
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G014116_T02 (Zea mays), 5'ss of exon 8
TCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatgt-tgctttcaggatta--caaattatcat--------ggttt---ttaatgttctttctaattcctacttttgctgt--ttggatgggaatag---
|||||||||| |||||| | || ||||||||||| ||||||||||||||||||||||| ||||| || || ||||| || || || || ||||||||| |||||  | ||| || |||||  |||   | ||| || |         |||||   | |||| ||   ||| || ||  |  ||||||  |  |||||||| |    
TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCAAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacaatctgtatgttttcaaaattgatctaataataactccaggtgggtttatctcaatgatcac-ctattttcttttcctgctgtaatgtgatgggaaaaaaag

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 8
TCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatgttgctttcaggatt-acaaattatcatggtttttaatgttctttctaattcctacttttgctgtttggatggga-atag---------
|||||||||| |||||| | || ||||||||||| |||||||| |||||||||||||| ||||| || || ||||| || || || || ||||||||| |||||  |    || || ||  ||  |     || |       |   |  |||   ||||  ||  |||| |||||  |||| ||  | |         
TCTGTTGGTACTTGGTGCTAGCACCTCATGATCCTATGCAATCGAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacagttgaatgtttgcaaaatggatctcataactccaggctggcttatctcaataatcactttttttcctgttgtgatgtgacgtgggggaaaaag

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G468717_T01 (Zea mays), 5'ss of exon 8
TCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatgttgctttca----ggattacaaattatca---tggttt---ttaatgttctttctaattcctacttt--tgctgtttggatgggaatag---------------
||     |  |   |  |  |      | ||||| |||||||| |||||||||||||| ||||| || || ||||| || || || || ||||||||| ||||| ||    || || ||    ||||  || |    ||   ||| ||   | |||  ||  | |  |||||| | |  ||   | |||  |  ||  |               
TCCAAAAGATTGAAGCCTCTGAAGTGAACGATCCTATGCAATCGAGCCTTCTCAATGCTACACTAGAGGATAAAAACCTTTCAGAAATCCCAAATTTCAGgtacatttgaatgtttgcaaaatggatctcataactccaggctggcttatctcaataatcactttt-ttcctattgtgatgtgatgtgggggaaaaaggttattgctgaagcag

upper sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 5'ss of exon 8
TCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatgttgctttcaggattacaaattatca-----tggtt-tttaatgttctttctaattccta--cttttgctgtttggatgggaatag---------
|||| ||||  ||||| ||||| |||||||| || |||||||||||| | |||||||| || || |||||||| ||| | || || || ||  |||||  |||  || | ||   |     |||      | |||     || || |||  |  ||       |||  |  |||||  | ||||  ||  |  |          
TCTGCTGGTTCTTGGTCTTGGCACCTCATGACCCAATGCAATCAAGCTTGCTCAATGCAACTCTGGAAGACAAGAATTTATCAGAAATCCCTGATTTCAAgtatattttattttctgataaattttgttatttcaataactgattcttttgtactcaaatgggttctcagtctttttttctttgtttgatatcacccgtttcag

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|29664483|gb|CB660758.1|CB660758
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|2311390|gb|C27545.1|C27545
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|29664786|gb|CB661061.1|CB661061
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|5002921|gb|AU068030.1|AU068030
EST:     ACACTCGAGGCCAAAAATCTCTCCGAGATNCCAAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCT
genomic: ACACTCGAAGACAAAAATCTCTCCGAGATACC-AAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCT
EST: gi|29639942|gb|CB644951.1|CB644951
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|4715022|gb|AU056139.1|AU056139
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|29678375|gb|CB674650.1|CB674650
EST:     GATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: GATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|5803423|gb|AI978393.1|AI978393
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCTGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|29645308|gb|CB650315.1|CB650315
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|29658197|gb|CB654472.1|CB654472
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|6799243|gb|AU082194.1|AU082194
EST:     GCCACACTCGAAGCCAAAAATCTCTCCCGAGATNCCAAATTTCCG                         GTTACTGTTGAAGCAACCTTGTAACCATGNAGGTGATTCAGTGGACAAGCT
genomic: GCCACACTCGAAGACAAAAATCTCT-CCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAA-CTTGTAACCATGGAGGTGATTCAGTGGACAAGCT
EST: gi|33797492|gb|CF324606.1|CF324606
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTA-CCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|300215653|gb|HO088279.1|HO088279
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCTGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|29637545|gb|CB642554.1|CB642554
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
EST: gi|29620777|gb|CB625788.1|CB625788
EST:     CTCAATGCCACACTCGAAGACAAAAATCTCTCTGAGATACCAAATTTCCG                         GTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT
genomic: CTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatg ... atgggaatagGTTACTGCTGAAGCAACTTGTAACCATGGAGGTGATTCAGTGGACAAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTGTTGGTATTTGGTGTTGGCGCCTCATGATCCGATGCAATCAAGCCTTCTCAATGCCACACTCGAAGACAAAAATCTCTCCGAGATACCAAATTTCCGgtacgttatgttgctttcaggattacaaattatcatggtttttaatgttctttctaattcctacttttgctgtttggatgggaatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA