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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaactcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG

Basic information

species Oryza sativa
transcript LOC_Os05g11140.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 6
gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaa------ctcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
             |  |||||    ||| | ||  | |   ||||| | ||||| ||  ||  | | |||  ||||||||      ||||| |||||| |||||| || ||||| ||||| || ||||| ||||||||||||||| | ||||| |||||  ||||||| ||||||||||| ||||||||||| ||||
------------gtacctgatgtagtctagtcaaaggatagtaata-tattttgtatactgtgtatagaatgatagctaaagaaatctcttgtttatgatagGTACGTCCATGGAGATGTGAAGCCTGAAAATTTTTTGCTTGGACCTCCAGGCACCCTACAAGAGAAGAAACTTTTTCTCGTTGACCTTGGTTTAG

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 6
------gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgt-tgcattttgaaatatagctaactcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
       | || || | ||  ||  |  | | |          |  |  |||  | | |  || | |  ||||  |  || |      ||    ||||   || ||||| || |||||||||||||||||||| ||||||||||||  ||| ||||| || || || || ||  | ||||| ||||| ||||||||||
gatggattgttggtatattgatcgcacacacacacacacacacacacacatatatatatatatatatatatttcaagttagaatggtgtc---attattgcagATATGTACACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACTCCCTGGAACTCTTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 6
gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatg-ttgcattttg----aaatatagctaactcttat-------ttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
          ||  |   |   |       ||      |  |  |  ||||| | ||| |  ||||| |    ||  | |  | |   ||||       ||||   || ||||| || |||||||||||||||||||| |||||||||||| |||| ||||| |   | || || ||  | ||||| ||||| ||||||||||
--------agttagcatggtatcagcagcagctacatggattgttcatttttggtatgatcacatttcgttgcaagaacatttcatctttatgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTTGGACCCCCTGGAACTCCTAATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 6
----gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaat-atagctaactcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
       || |  |  |    | |||  ||    | | ||  |  || |  |    |  ||||||||     |  | ||   |      |  ||||   || ||||| || |||||||||||||||||||| |||||||| ||| |||| ||||| |  || || || ||  | ||||| ||||| ||||||||||
atgtaagttagcatggtatcatcatcagctacatggattgtggtttattgatcacat-tatgttgcaagaatatttcatcattctgctgtcattattacagATATGTGCACGGTGATGTAAAACCTGAGAACTTTTTGCTGGGACCCCCTGGAACTCCTGATGAAAAGAAGTTGTTTCTGGTTGATCTTGGATTAG

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 6
gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaactcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
         |  || ||| ||  |       | || |  |    |  |    ||  | ||   |  | | |   ||    ||| | ||| |   || ||||| ||||| ||||||||||| ||||||||| |||||||  | || ||||| |  ||||||||||||||||| ||||| ||||| || ||||
--------gtaattttctaatatttctgctactgtaactctctttcttcaagtggtttttatttgctaagaagcagt--gctcctgtttctac-agATATGTGCATGGCGATGTAAAACCAGAGAATTTTCTGCTTGGGCCTCCTGGAACTCCTGAAGAGAAAAAACTTTTCCTTGTAGACCTCGGCTTAG

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 6
gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagc--taactctt---atttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
                                          || |         |      || | |   | |     | |||| |   | || ||  |||||||| ||||| |||||||| |||||||| |||||||||||  | ||||||||    || ||||||||||| ||||||||||||||||||||||
-nnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnnaaaaaaaaaaaaaaaaaaaagatatagtgctgttataatgactcctgcaacttctggcagGTATGTGCATGGGGATGTAAAGCCTGAGAACTTTTTGCTTGGTCCTCCAGGAACTAATGAGGAGAAAAAACTGTTTCTTGTTGACCTTGGATTAG

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|29681938|gb|CB678213.1|CB678213
EST:     TGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGG                         GTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGG
genomic: TGTATTGCTATAGAAGCAATCTCCATATTGGAGAAGATGCATTCGAAAGGgtatttgttt ... tttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatagttttttgcatgttgcattttgaaatatagctaactcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG
                                 agctaac  putative branch site (score: 2)
                                       ctcttattt  CT-rich tract
                     attttgaaatata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgtttttttctctgatcctctcttggcagtgaagcctaatagttttttgcatgttgcattttgaaatatagctaactcttatttatgttagGTATGTTCATGGTGATGTAAAACCTGAGAATTTTTTGCTTGGAACCCCAGGAACCCTGGAAGAGAAAAAACTTTTTCTTGTTGACCTTGGATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA