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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taccttttttcttttctttttattcttatttctagcttatagttctcttctttctgtcacacacctaaaatggccattgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA

Basic information

species Oryza sativa
transcript LOC_Os02g57660.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G374973_T01 (Zea mays), 3'ss of exon 3
taccttttttcttttctttttattcttatttctagctta--tagttctcttctttctgtcacacacctaaaat---ggccattgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
     || ||    | || || || ||  | ||  ||||  |  |  | ||||||||||  || ||    | |      ||  ||    ||   || ||  |||| |||||||| |||||||||||||||||||||||||| ||||||||||| ||||| ||||| ||||| |||||| |  ||||||| || ||||||||||||
---tcttgttgacatattcttgttgtttctcctgacttaatttataatgttctttctgttccagactcgtactttaaaacacagtatcaatccaatctt--gtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGCGGAAACTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA

upper sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G050309_T01 (Zea mays), 3'ss of exon 3
--------------------------------------------------------------------------------taccttttttc----ttttctttttattcttatttctagcttatagtt--ctcttctttctgtcacacacctaaaatggccattgttcttatt--ttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
                                                                                 |||| || |     | |||||||| || ||  | || ||||| | |   || ||||||||||  |   |  || |     |       ||||  |    |||||||| |||||||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| |||||| |  ||||||| || ||||||||||||
gtccgcatttcttaaaaaaatatggtcttatccactgcaaattgagtgacatttagattgtacagaattttgttcattgggacctcttgttgacatattctttttgttgtttctcctggcttaaaatatactattctttctgttcctggctcaatactttaaaacacaatattgatccacttttgtagGAATTTGAGAGAGATGTTCAAGATTGATGCTGCAGACTATATGATCTCCATATGTGGAAATTCTGCTCTTAGGCAACTATCTTCCCCTGGAAAGAGTGGA

upper sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA03G34340.1 (Glycine max), 3'ss of exon 2
taccttttttcttttctttttattcttatttctagcttatagttctcttctttctgtcacacacctaaaatggccattgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
|    || |      || ||    || || | |  ||| |  ||||    ||    |  || |  |    | |  ||     |      |  | ||| ||||||||||| ||| ||||||||||||||||||| ||||| ||||| || || ||||||||   | | || |||||  |||||||||| || || ||||| 
tgttcttatagacaactgttacagctcatctttctcttctctttcttcctttcacttttcataagtttgttagatataaccttctagagacctgttgcagAAATTTGAGAGAGCTGTTCAAGATTGATGCTGCCGATTACATGATGTCCATTTGTGGAAACGATACTCTGAGGGAACTATCTTCTCCGGGGAAAAGTGGT

upper sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA10G06800.1 (Glycine max), 3'ss of exon 3
taccttttttcttttctttttattcttatttctagcttatagttctcttctttctgtcacac-acctaaaatggccat-tgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
    |       |    ||  || |   ||| |  ||| |   | | |  || || ||||   || |   || |  || | |     | | |  | ||| ||||||||||| ||| ||||||||||||||||||| || |||||||| || || |||||||||  ||| || |||||  | ||||||||||| || ||||| 
--agtaaggaactactgttacatcccccttttttccttctctctttttcattcctttcactttacatgtgattgttatatatgaccttgtgacctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAATGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT

upper sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA13G20980.1 (Glycine max), 3'ss of exon 3
taccttttttcttttctttttattcttatttctagcttatagttctct-tctttctgtcacacacctaaaatggccattgt-tcttatttt---attttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
     |   |  |        ||| |||   |   ||| |  |  ||| |||||   |  |||     |  ||    |||| | | |  ||   || | ||| ||||||||||| ||| ||||||||||||||||||| || |||||||| || || ||||||||   ||| || |||||  | ||||||||||| || ||||| 
-----tacatagtaaggaaccattgttacagccccctttttttcttctctcttttcctttcactttgcatgtgattgttgtatatgaccttgtgatctgttgcagAAATTTGAGAGAGTTGTTCAAGATTGATGCTGCTGACTATATGATGTCCATTTGTGGAAACGATGCTCTGAGGGAACTTTCTTCTCCAGGGAAAAGTGGT

upper sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
lower sequence: AT3G09920.1 (Arabidopsis thaliana), 3'ss of exon 2
taccttttttcttttctttt-tattcttatttctagcttatagttctcttctttctgtcacacacctaaaatggccattgttcttatt-ttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
    ||    ||| | |  |  || ||| |||||   |  ||  |    | |    ||      | |     ||   || |  | |||  ||    |||||||||  ||||||||||||||||||| ||||| || ||||||||||| || || |||||||||  | |  | || ||  | ||||||||||| ||||| || 
---gttagaacttgtgtactgcatacttttttcttagtagtatgttaactatagtagttgtgtcctt-----ggtgtttatattcattgctaaaccttgtagAAACCTGAGGGAGATGTTCAAGATCGATGCAGCTGATTATATGATGTCCATTTGTGGAAATGATACTTTAAGAGAACTTTCTTCTCCAGGGAAGAGCGGC

upper sequence: LOC_Os02g57660.1 (Oryza sativa), 3'ss of exon 3
lower sequence: PP1S311_23V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------------taccttttttcttttc---tttttattcttat--ttctagcttatagttctcttctttctgtcacacac----------------ctaa--aatggccattgttcttattttat-----tttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
                                              ||| | ||||| ||||   |||| |   ||||  |  |   || |  |||| |  ||||  | | | |                  |||  ||   || |   | || ||  ||     || | | ||| ||||| |||| ||||||||||||||||| |||||||| ||| | ||| |||||||| ||  |||  | |||||| |   ||| || ||||||||||| 
gtcacacactactctttttatggggtgaattttttcacggatcaaatacttgttttcatttcaatttttcagcgttatgatcttcatttctttttctttcttttccttaaaaaagggagtattggagaatgttaatgaacaaccctgaatgttgttaaataaatgttctggcagACATTTGCGGGAAATGTTCAAGATTGATGCAGCAGATTACATGTTATCTTTATGTGGAGATGATGCGTTGAGGGAGCTTGTTTCACCTGGAAAGAGTGGC

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|58605144|gb|CK033177.1|CK033177
EST:     CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAG                         AAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
genomic: CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAGgttcattgca ... ttttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
EST: gi|58666178|gb|CK054864.1|CK054864
EST:     CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAG                         AAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
genomic: CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAGgttcattgca ... ttttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
EST: gi|58608242|gb|CK036275.1|CK036275
EST:     CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAG                         AAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
genomic: CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAGgttcattgca ... ttttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
EST: gi|58606811|gb|CK034844.1|CK034844
EST:     CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAG                         AAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
genomic: CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAGgttcattgca ... ttttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
EST: gi|88307423|gb|CI642071.1|CI642071
EST:     CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAG                         AAATTTGAGGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTA
genomic: CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAGgttcattgca ... ttttttgtagAAATTTGAGGG-AGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTA
EST: gi|58612782|gb|CK040494.1|CK040494
EST:     CATCCTGCAGAAGACTTCAAATGGAAGGACTATNGTCCCATGGTTTTCAG                         AAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
genomic: CATCCTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAGgttcattgca ... ttttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
EST: gi|58688826|gb|CK077513.1|CK077513
EST:     CTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAG                         AAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT
genomic: CTGCAGAAGACTTCAAATGGAAGGACTATTGTCCCATGGTTTTCAGgttcattgca ... ttttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttctttctgtcacacacctaaaatggccattgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA
                 acctaaa  putative branch site (score: 3)
                                  ttcttattttattttt  putative PPT
                              attgttcttattttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taccttttttcttttctttttattcttatttctagcttatagttctcttctttctgtcacacacctaaaatggccattgttcttattttattttttgtagAAATTTGAGGGAGATGTTCAAGATTGATGCTGCAGATTATATGATCTCTATATGTGGAAATTCTGCACTTAGGGAGTTATCTTCTCCAGGAAAGAGTGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA