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

gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA

Basic information

species Oryza sativa
transcript LOC_Os05g11140.2
intron # 2
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 2
lower sequence: GRMZM2G116151_T03 (Zea mays), 3'ss of exon 2
gtcagctcttctaatccggatgtctttttc---atttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
              ||   ||| ||| |     ||||  |  | |||   ||| ||| ||||||   ||  ||| |||| || |||| |||| ||||| |||||||||||||||||||||||||| ||||| ||||| ||||| ||||||||||||||||||||
-------------gtctttatgccttctctggaatttttaattgtaattcatcgtagctgcattagcataaacgttttttttcatactagGTTGCAATCAAATTTGAACATCGAACCAGCAAAGGTTGCAACTATGGTGCTCCTTATGAGTGGCAAGTTTACAA

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G09190.1 (Glycine max), 3'ss of exon 2
gtcagctctt--ctaatccg--gatgtctttttcatt------tccatatttaaaatatcatagttgcatttatattcacgcttttctttatac----cagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
||  | | ||   || |  |  ||| | | |||  ||      |  ||  || |   ||  | | |   |   |||| |||  || || |||       |||| ||  |||||||||| ||| ||| |||||| || |||||||||||| |||| ||||||||||| ||||||||
gtatggtgttggttagtgtgttgatatttatttggttaaagagtgtatgatttatgcatattggatttgtcgttattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAGGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G09070.1 (Glycine max), 3'ss of exon 2
-------gtcagctcttctaatc-cggatgtctttttcatttccatatttaaaatat-catagttg------catttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
       || || |    |  |    ||| | |  || |      | ||| |   || |||| | |      ||||  ||   |   || | || ||   || | ||  |||||||||| ||| ||| ||||||||| |||||||||||| | ||  |||||||||| ||||||||
gtatggtgttagttagggtgttgattgatatttggttaaagagtgtgtttgactgatgcatattggatatgtcattggtacgtattgttctattgattgtagATAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCCCCACATGAGTGGCAGGTTTACAA

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA04G09080.1 (Glycine max), 3'ss of exon 2
gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttat----attcacgcttttctttatac----cagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
||  | | ||    |   ||| | |  || |      | ||| |   ||     ||| |||| |    ||| |||  || || |||       |||| ||  |||||||||| ||| ||| ||||||||| |||||||||||| |||| ||||||||||| ||||||||
gtatggtgttagcgtgttgatatttggttaaagagtgtgtttgattgatgcatattggatttgtcattattgacgtattgctctattgattgtagGTAGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCTCCATATGAGTGGCAGGTTTACAA

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: AT2G25760.2 (Arabidopsis thaliana), 3'ss of exon 2
gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
||  ||| ||    |  | | || |  ||  ||||  |   |    | | ||   |    | || || | |  |    || |   |||||||  | || ||||| ||| ||||||||||||| || || |||||  | || ||||||||||||||||||||
gtatgctgtttgtgtttgcaagtttacttgctttcttttggttttctgtgatctgtaatgtgattttgatgtgtccacttttgt-agGTGGCTTTGAAGTTTGAGCATAGAACCAGCAAAGGATGTAACTATGGGCCACCGTATGAGTGGCAAGTTTACAA

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv04s0008g00160.t01 (Vitis vinifera), 3'ss of exon 2
---------gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagt-tgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
          |  |   || |  | |          |    |    |||      | | ||  | |  || | | |||     ||  |  ||   |||| ||  |||||||||| ||| ||| ||||||||| |||||||||||| | || ||||||||||||||||||||
gtgtaacatttatgactttgtggtacaatcactcaatgtggtgatctatgctgggttttatcttgttaatatgttttctgatcttcatgaattttagGTTGCCTTAAAATTTGAGCATAGAAGCAGCAAAGGGTGCAATTATGGACCACCATATGAGTGGCAAGTTTACAA

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: PP1S66_174V6.1 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------gtc--agctcttctaat-ccggatgtctttttcattt--ccatatttaaaatatcatagttgcatttata--ttcacgcttttctttatac---cagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
                                   |||  |   | | || | |||   ||  |  | ||||  | |   |       |  |   || |  || |   | |  ||| | ||  | |   ||||| ||  |||| ||||||||||| | |||||| || |||||||||||  |||| || |||||||||||||||||
gtactctttactctaattcgttgaggtccggtcgtgtcgtattccgtatagtgccgagggttgtgattatttagcgagtatctttgctttgtgtctggaagtacaaactgagtcttgttttcgtgctcgcagGTAGCTTTAAAGTTTGAACATCGGAGCAGCAAGGGTTGCAATTATGGTCCTCCTTACGAGTGGCAAGTTTACAA

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ38433 (Selaginella moellendorffii), 3'ss of exon 2
gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
                  ||    |     |||| |  | ||  | |  |    ||    | |    |          |  |  ||||| ||  | || ||||||||  ||| ||| ||||| ||||| |||||  |||| ||||||||||||||||||| 
---------------gtagactgttcgaagatttgctcagttggattggctctttt---ctcagcggctgatcaaagatgttgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

upper sequence: LOC_Os05g11140.1 (Oryza sativa), 3'ss of exon 2
lower sequence: EFJ31718 (Selaginella moellendorffii), 3'ss of exon 2
gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcattta-tattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
                  ||    |     |||| |  | ||  | |    |  |  ||     |  |||    | |     |  ||||| ||  | || ||||||||  ||| ||| ||||| ||||| |||||  |||| ||||||||||||||||||| 
---------------gtagactgttcgaagattttctcagttggattgctcttttctcagcggctgatcaaagatgt-----tgtcagGTTGCTTTGAAGTTTGAACACAGAAGCAGTAAAGGATGCAACTATGGGCCTCCGTATGAGTGGCAAGTTTACAC

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:     TTTCCTCTCCTGGTGTTACCGACAGGACACCTGGAGCAAATGCTTTGGAG                         GTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCT
genomic: TTTCCTCTCCTGGTGTTACCGACAGGACACCTGGAGCAAATGCTTTGGAGgtcagctctt ... tttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA
                                 ttcacgcttttcttt  CT-rich tract
     tatttaaaatatcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagctcttctaatccggatgtctttttcatttccatatttaaaatatcatagttgcatttatattcacgcttttctttataccagGTGGCAATAAAATTTGAACATCGAACCAGCAAAGGCTGCAATTATGGAGCTCCCTATGAGTGGCAAGTTTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT