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'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG

Basic information

species Oryza sativa
transcript LOC_Os05g38150.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G094309_T01 (Zea mays), 3'ss of exon 4
gtgtgtatgcaattctat----attttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
||| |  |   ||  |||    ||  | |  |      ||   | |||  | |||||| | ||||||||| | |||||| ||||||| ||||||||||||||||||||||| || |||||||| || || ||||||||||| ||||||||||| ||||||||||| |||||||
gtgagcgtaatatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGTAGCAATAAGCTGGTTTCACAAATCAAGGCATCAACTAAGATCCCTGTTCTTGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AC203754.4_FGT008 (Zea mays), 3'ss of exon 11
----------------------gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaa---------acccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
                        |||   | ||   |||||| | |||  | ||||  ||||| | || ||||         || | ||||||||| | |||||| ||||||| ||||||||||||||||||||||| || |||||||| || || ||||||||| | ||||||||||| ||||||||||| |||||||
acgaaaattgctgatttactaaaggtgagcgtaa---tatattatgaaaatgatgattgtaccattatgcctaataagcctaaactcataatacactctacagCTTCATGATGTAATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCACAAATCAAGACATCAACTAAGATCCCTGTTCTTGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G375504_T03 (Zea mays), 3'ss of exon 11
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttgg---------ctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
  ||   || ||   |||||  | |||    |||| |||||||| ||          |||||| | |||||   | | |||||||||||||||||||||||||||||||||||||| || |||||||| || || |||||||| || ||||||||||| ||||| || || ||||| |
--gtaagtgtaa---tatatcatgaaaataatgattctaccaatatgcatgataagcctaaactcataatatgttctacagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGCAGCAATAAGCTGGTTTCGCAAATCAAAGCATCAACTAAGATACCTGTCCTCGGTCATGCGG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA01G24530.1 (Glycine max), 3'ss of exon 13
-------gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtg---cagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
        |   ||   ||   || ||  ||| |    |  |  ||| |   ||| |   | | || || ||| ||   |||||||||||||| || ||||| ||  | || ||||| |||||||||||||| |||||||||||||  ||||| || |||||||||||||| |||||||
gttggatatcactagtaaaaaataaatcctcataattattgttttacaa---tggtttgtcacttattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA03G12240.1 (Glycine max), 3'ss of exon 12
-------gtgtgtatgcaattctatattttcaaagcgttgatactacca--atttggctaaacccgtaatacactgtg-cagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
        |   ||   ||   || ||  |||||    |  |  ||| |  ||||| |   ||   | |||| ||||  |||||||||||||| || ||||| ||  | || ||||| |||||||||||||| |||||||||||||  ||||| || |||||||||||||| |||||||
gttggatatcactagtaaaaaataaatcctcaaaattattgttttacaatgatttgtc---actaattatactctgtctcagCTTGATGATGTAATAGATCTAGTGGTCCCTAGAGGCAGTAATAAGCTTGTTTCTCAAATCAAGGAATCAACAAAAATTCCTGTTCTTGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA18G40770.1 (Glycine max), 3'ss of exon 13
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgt-gcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
                | |||   |||   |   |      |||     | |||   | ||||  ||   ||||||||||| || || ||||||||  | || ||||| ||||| || ||||| |||||||||||||  || || ||||||||||||||||| |||||||
-------------gtaaaattcctaaaatttatttgtctgaaatgattttcaactaattatactttgccacagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAACAAACTTGTTTCTCAAATCAAGGATTCCACAAAGATTCCTGTTCTTGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA14G07120.1 (Glycine max), 3'ss of exon 9
----------gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactg--tgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
            ||| |    | | |  ||||   |||| |    |||   |   | |   | |    |||||      | ||||| ||||| || |||||||| || ||||||||||| || || || ||||| ||||||||||||   || ||||| ||||||||| | || || ||||
gtgaactaatcagtggagcttaatttcaatttcataagcctgttcactttaagcattggccacctttaaatacttaaatttcagCTGGATGACGTAATTGATCTGGTGATTCCAAGAGGCAGCAACAAACTTGTTTCTCAAATCAAGAGTTCCACTAAAATTCCTGTTTTAGGTCACGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: GLYMA07G16510.1 (Glycine max), 3'ss of exon 9
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
       |  |||||   |  || |      ||| |  |    ||   ||||   | || |   |    ||||||||||| || || ||||||||  | || ||||| ||||||||||||||||||||||||||||   |||| ||||||||||||||||| |||||||
------gtaaaattcctaaaatttattagtctgaaatgatt--ttccactaa--tcatactttgcc--acagcttgatgacgtgatagATCTTGTGGTCCCCAGAGGCAGTAATAAGCTTGTCTCTCAAATCAAGGGTACAACAAAGATTCCTGTTCTTGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G39800.4 (Arabidopsis thaliana), 3'ss of exon 12
------gtgtgtatgcaattctatattttcaaag---cgttgatactaccaatttggcta-aacccgtaatacac---tgtg---cagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
           | | |||      |  | |||     | ||  ||       ||   ||  |||||   ||   |   ||||   ||||||||||| || || |||||||| || ||||||||||| || ||||||||  |||| || ||     | || || || ||||| || || |||||||
gtaagaacagatttacaagctaggagctgcaacagttcttttgtatcttttgttaaactggaacccaccatttgcatttgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT3G55610.2 (Arabidopsis thaliana), 3'ss of exon 12
------------gtgtgtatgcaattctatattttca-aagcgttga--tactaccaatttggcta-aacccgtaat--acact----gtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
             |   |||| |||   |  |   || ||| | | |  |  |  || ||   ||  |||||   ||  ||| |    || ||||||||||| || ||||||||||| || |||||||| || || |||||||| |||||||| ||    || || || || || || || || |||||||
gtaagcagatagatacatatg-aatggcaagtccccagaagtgattagcttttttcacttatactggaacccaccatttacatttttggtacagCTTGATGACGTTATTGATCTTGTGATCCCAAGAGGCAGCAACAAGCTTGTTTCTCAAATAAAAAACTCGACGAAAATCCCAGTGCTAGGCCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: AT2G39800.3 (Arabidopsis thaliana), 3'ss of exon 12
------gtgtgtatgcaattctatattttcaaag---cgttgatactaccaatttggcta-aacccgtaatacac---tgtg---cagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
           | | |||      |  | |||     | ||  ||       ||   ||  |||||   ||   |   ||||   ||||||||||| || || |||||||| || ||||||||||| || ||||||||  |||| || ||     | || || || ||||| || |         
gtaagaacagatttacaagctaggagctgcaacagttcttttgtatcttttgttaaactggaacccaccatttgcatttgtgttacagCTTGATGACGTTATCGATCTTGTGATCCCAAGAGGAAGCAACAAGCTTGTTACTCAGATAAAAAATACTACAAAAATCCCTGTGCTAG---------

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv13s0019g02360.t01 (Vitis vinifera), 3'ss of exon 12
-----------------------------gtgtgtatgcaattctatattttcaaagcgttgatactaccaatt--tggctaaacccgtaat----acactgtgc---agCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
                              |   ||   |  | |  | ||||| |  | |||||  |  |||   ||   | || |   ||        |||||   ||||||||||||| || || ||||| || |||||||| || ||||| ||||| |||||||| ||||  ||||| || ||||||||||| || |||||||
gtgagctgatgtgctgagaatgatcattgatagttaaaaacatttgaactttcagaatggtgatatgaaaaatggatgttcacactcagtatttttgttttgtgctccagCTTGATGATGTGATCGACCTTGTAATCCCAAGAGGCAGCAATAAACTTGTTTCTCAAATAAAGGATTCAACAAAAATTCCTGTTCTGGGCCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: Vv08s0007g01060.t01 (Vitis vinifera), 3'ss of exon 12
gtgtgtat-gcaattctatattttcaaagcgttgatactaccaatttggcta--aacccgtaata-cactgtgc-agCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
||| | || |  |||  |||| ||  | | |||  |  ||  |  |||| ||  |||  ||  ||   |||  | |||||||||||||||| |||||||| || || ||||| || || || || || |||||||||||||  |||||||| || ||||||||||| |||||||
gtggggattgagattggatatgtttgatg-gtttttcataataggttggttattaacttgttttagttctgccccagCTTGATGATGTCATAGATCTTGTGATCCCTAGAGGCAGCAACAAACTCGTTTCTCAAATCAAGGATTCAACTAAAATCCCTGTTCTTGGTCATGCTG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ17662 (Selaginella moellendorffii), 3'ss of exon 12
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
                    |  | |  | ||  | ||   |  | |  |     | ||  |     | |||||||| ||||| ||||| || || || ||||||||||| ||||| ||||| || |||||||||| ||| || || |||||||| || || ||||| |
-------------------gtaactatactttcgtgctgttagctcgttt-----cttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG

upper sequence: LOC_Os05g38150.1 (Oryza sativa), 3'ss of exon 11
lower sequence: EFJ29127 (Selaginella moellendorffii), 3'ss of exon 12
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
                          | |  |  |  |      || |||     | ||  |     | |||||||| ||||| ||||| || || || ||||||||||| ||||| ||||| || |||||||||| ||| || || |||||||| || || ||||| |
------------------------gtaactatacttttgtgctgttagctcgtttcttaccatgggtttcagCTTGACGATGTTATTGACCTCGTTATACCAAGAGGAAGCAATAAACTTGTTTCACAAATCAAGGAGTCTACGAAAATTCCTGTGCTGGGCCATGCCG

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|88839043|gb|CI377967.1|CI377967
EST:     AACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAG                         CTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTC
genomic: AACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgc ... cactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTC




















RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 70 (downstream exon)
Score: 37

GTTATAACTGATGCTATTCCTCGTAATGTTGGTGAAAAACTTATTGGCCTTGTTACAACTAGAGATGAGATCGCAGATTTGCTAAAGgtgtgtatgc ... cactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG




<











<


<











 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG
                             ggctaaa  putative branch site (score: 37)
                                        taataca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtatgcaattctatattttcaaagcgttgatactaccaatttggctaaacccgtaatacactgtgcagCTTGATGATGTCATTGATCTTGTCATTCCAAGAGGAAGTAATAAGCTTGTCTCTCAAATCAAGGCGTCAACTAAGATTCCTGTTCTTGGGCATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG