Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA

Basic information

species Oryza sativa
transcript LOC_Os01g62040.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G018697_T02 (Zea mays), 3'ss of exon 3
----------------------------------gtaagcacatagttttagctagttttttaagtttgtgcaaggat-agtgttcttgaattacgttttcaca--------ctcattcataactgatacggta---ttcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
                                     |  ||   | | ||  |   ||  | | ||  |  |   || | || | || | |  || ||| | |          || |     ||  ||   ||   || |||||||  |  |||| ||||| ||  | | ||| | |  ||  |  ||||||||||||||||| |||||||| ||||||||||||||  ||||||||| ||||||||||||||||||||||||  |  | |||||||| ||||||||||
gtaagcaatggatatatgcccatgtccaagttaaacgaatactaggctataattgcattagtgatttcctttatttatcaatggttttcattatcgctttgatagctgatgttccacttcgtgcttctataataaatttaccattgttag--tctataataa-atttaccagtgttgctctgt-tcctagGTTACTGAACTTTCCCCAGAAGAGGCTGAGAGTACAACTGGTGGATATGCAAAAAGCATTAGCCATGTAATCATCAGCTTAAAGACTGTTAAAGGGACTA

upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G032267_T02 (Zea mays), 3'ss of exon 3
gtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggta-----ttcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
                                            |||| | ||  |||   || ||| |||  ||||| |  | |  ||||     |   || |   || ||||| ||||  ||| | |  || | |  ||  |  ||||||| ||||||||| |||||||| |||||||| |||||  |||||||||  |||||||||||||| |||||||| ||  | |||||||| ||||||||||
--------------------------------------------agtggtttt--atttatttatca-actgtttcattatcgctttggtagctaatgttcacttcttgcttctataatag-atataccaatgttgctctgt-tcctagGTTATTGAACTTTCCCCAGAAGAGGCTGAGAGCACAACTGGTGGATATGCGAAAAGCATTAGCCACGTAATCATTGGCTTAAAGACTGTCAAAGGGACTA

upper sequence: LOC_Os01g62040.1 (Oryza sativa), 3'ss of exon 3
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 3
gtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtc-tgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA-------
                                || | ||  |||  ||   ||   ||  |||   |   | | |    | | |||   |  ||   ||||  | ||   |   | | || ||   |    ||      |||||||| || ||||| || ||||||||| ||||||| |||||| |||| ||||||||||||||||||||||| || || ||  | || ||||| || || || |       
-------------------------------gttat-cactgattatgagttt--tttttgttaatagtttgacttgccagtaatatcatgatctttttgttgtattatcatctttaaatcaagtagcttctc----ttttttaggtgacagAACTCTCCCCAGAAGAAACTGAGAGCACAACAGGTGGTTATGGAAAAAGCATTAGCCATGTGATTATTGGATTAAAAACTGTGAAGGGAACCAAGCAGCT

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|33675973|gb|CF304212.1|CF304212
EST:     GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAG                         GTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA
genomic: GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacat ... tgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA
EST: gi|33676830|gb|CF305069.1|CF305069
EST:     GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAG                         GTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA
genomic: GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacat ... tgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA
EST: gi|88956452|gb|CI092705.1|CI092705
EST:     GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAG                         GTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA
genomic: GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacat ... tgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA
EST: gi|33676655|gb|CF304894.1|CF304894
EST:     GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTCATGAAGGAGAG                         GTTACTGAACTT
genomic: GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacat ... tgccttttagGTTACTGAACTT
EST: gi|33674769|gb|CF303008.1|CF303008
EST:     GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAG                         GTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA
genomic: GAGCTATAGGCTTGCGTATAAAAGAAAATAAAGAGGTTTATGAAGGAGAGgtaagcacat ... tgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA
                ttctaaa  putative branch site (score: 2)
                                       cttcattgcctttt  putative PPT
       attgtctgtttctaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcacatagttttagctagttttttaagtttgtgcaaggatagtgttcttgaattacgttttcacactcattcataactgatacggtattcccattgtctgtttctaaaataatataaaactgtgcttcattgccttttagGTTACTGAACTTTCGCCAGAAGAAGCTGAGAGTACAACAAGTGGATATGGAAAAAGCATTAGCCATGTAATCATAGGTCTGAAGACTGTAAAAGGGACTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA