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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag

Basic information

species Oryza sativa
transcript LOC_Os06g45120.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA08G23990.1 (Glycine max), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactat-tcctctctatttgataact-----gctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag
||| |||||||| || || |||||||||||||| || |||||||| || |||||||| ||||||||||| |||||||||||||||||||| ||||| |||||    | | |||  ||| |  |    |||| |       |     |   |   |  |||   |||||      ||  |   |  ||  ||  | |                    
TGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATACCTGGAGCTTTTGGTTGTGGTAAAACTGTCATTAGTCAGGCTCTTTCTAAGgtgaacttaatataccctattaaaacaataattttttaattgaagatattctccgtaattcatctttttcctccacccacccccctgttttggcag--------------------

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA07G00430.1 (Glycine max), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag
||| |||||||| || || |||||||||||||| || |||||||| |||||||| || ||||||||||| ||||| |||||||||||||| ||||| |||||    | |  |  ||     ||  || ||    |    ||     | |  |||  ||||        | | |  | | | ||    |    || |              
TGTTCTTGATGCCCTTTTCCCCTCAGTTCTTGGCGGGACTTGTGCCATTCCTGGTGCTTTTGGTTGTGGTAAAACAGTCATTAGTCAGGCTCTTTCTAAGgtgaacttaaaacacccta--ataagacaatgatt--ttttaattgtagatattctcctt-------aattcatctttttcccccaaccacttgcag-------------

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G78900.2 (Arabidopsis thaliana), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag
||| |||||||| || || || || |||||||| ||||| ||||| |||||||| || ||||| ||||| |||||||| || |||||||||||||| ||||||  ||   |    ||||||  ||     |   |   ||| |      |  | |   |   ||  | |||   || | |   || | |                     
TGTTCTTGATGCCCTTTTCCCTTCTGTTCTTGGTGGAACCTGTGCCATTCCTGGTGCTTTTGGCTGTGGGAAAACTGTTATCAGTCAGGCACTTTCCAAGgtaccttg--tgacactctctggttttgttccattta-attactggatagattgaatttccaaagctaact---ttttcttatttacatag-------------------

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0054g00890.t01 (Vitis vinifera), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgt-attttcactattcctctct----atttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag
||| |||||||| || || || || ||||| || ||||||||||| || ||||| |||||||||||||||||||| ||||| ||||| || ||||| ||||| |  ||  || ||  || ||    |   || | |   |  || |    | | ||   |   | ||    |       || |       |  ||  || | || |   ||||||
TGTTCTTGATGCCCTTTTCCCTTCTGTTCTCGGTGGAACTTGTGCCATACCTGGGGCATTTGGTTGTGGAAAAACAGTCATCAGTCAAGCTCTTTCTAAGgtgagcttgtcttttattcacttgggaccagacatcctttgacaatatt-aggtgctacaaattctttccttattcatcttgtacttaaatgttgtgtgtacatgtac-atgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv04s0008g02580.t01 (Vitis vinifera), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag
||| || ||||| || ||||||||||| || || || |||||||| |||||||| |||||||| ||||| ||||| ||||| ||||| || ||||| ||||| | ||    |||  | | || | |     || |   | |     |||  || |  ||| ||      || | |    ||| ||  |  |      |  || | |||||
TGTTCTCGATGCTCTCTTTCCCTCAGTCCTGGGTGGGACTTGTGCAATTCCTGGGGCATTTGGCTGTGGGAAAACAGTCATCAGTCAAGCTCTTTCCAAGgtgtatttctcatt--tgtttactaggcttttgtttttaatatgt-tggaaataattcttctat-----ctcagtctcatgcattagcataacatctac-tcatttgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S44_102V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgc-ccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag-------------------------------------------------------
| |||| ||||| ||||| || || ||||||||||| ||||| || |||||||| |||||||| |||||||| |||||||||||||| || || || |||||| ||       ||   |    ||  |    | |    | ||  |||     ||  | ||||    |   ||  || |||   |   ||| | |||| |||  | || ||                                                       
TATACTGGATGCTCTATTCCCTTCTGTTCTTGGAGGTACTTGCGCCATTCCTGGTGCATTTGGATGTGGAAAGACTGTCATTAGTCAAGCGCTCTCTAAGgtagttggttacatctgtttggatttttcgaagttcatttcgcatcatacattttttctttttcttttctttgg-ttgtgtatttaagctg-cagaaactattgtttgaagtttgtatgaaagttctggaacgaggcttattttttgcaaatttgtttgtgtgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S8_312V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgt-attttcactattcctctctatttgataac-tgcta--gcattgcccatgggcat--tagccttttaaaatgac------tgaattctgtgc-ctttcctga----ctgaaaat-------atcttatgcag------------
| | || ||||| |||||||| || || || ||||| || ||||| |||||||| || || |||||||| ||||| || ||||||||||| || |||||||| |||  |   |      | | ||||   || |  ||  |||| | |  ||   |   ||   | ||    |||          || ||| |  || ||  ||    ||  ||||       || |||||               
TATTCTGGATGCTCTATTTCCATCTGTCCTCGGAGGTACCTGTGCAATTCCTGGTGCGTTCGGTTGTGGGAAAACAGTTATTAGTCAGGCTCTGTCAAAGgtgattggcttcaccttattgtgtttggagacatagtaaagcatcgtctttgtttaccataatttattgggttgataagctgcagatactgcgagctgtcacgatttccttgaaatggttctaattttatgtgctgctgtgtgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: PP1S10_201V6.1 (Physcomitrella patens), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattt--tcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag---------------------------------
  |||| ||||| || ||||| || || |||||||| || || || |||||||| |||||||||||||| || || ||||| ||||| |||||||| |||||| ||  |  | | |  | |  ||||  |   |   |        ||||||   |    | |     ||  |      | ||  |||||||    ||| |    |  | |                                  
AATACTGGATGCTCTGTTTCCGTCTGTCCTTGGAGGTACCTGCGCCATTCCTGGTGCATTTGGTTGTGGGAAGACCGTCATCAGTCAAGCACTTTCTAAGgtagttggttgcaactgat-tgaattttttgcatttcatttcatttcatgggatcttagttct----gtggtttttacttatgtttttcctg--caaaagtggtgttggtaatgacactcgactcatttaattgtttttgcgcag

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ30330 (Selaginella moellendorffii), 5'ss of exon 10
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag
  |  | ||||| || ||||| || || || || ||||| ||||||||||| ||||||||||| |||||||| || || ||||||||||| ||||| |||||||||  |   ||| | | || |   | ||   || | ||| |      ||                                                          
CATTTTGGATGCGCTGTTTCCTTCCGTGCTGGGGGGAACGTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttgga--gttcttttgtaatgcgtgac---taactttgtcatgaaacag---------------------------------------------------------

upper sequence: LOC_Os06g45120.1 (Oryza sativa), 5'ss of exon 10
lower sequence: EFJ33015 (Selaginella moellendorffii), 5'ss of exon 9
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag
  |  | ||||| || ||||| || || || || ||||| ||||||||||| ||||||||||| |||||||| || || ||||||||||| ||||| |||||||||  |   ||| | | || |   | ||||    | ||| |      ||                                                          
CATTTTGGATGCTCTGTTTCCTTCCGTGCTAGGGGGAACCTGTGCTATTCCGGGAGCATTTGGCTGTGGAAAGACCGTTATTAGTCAGGCGCTTTCGAAGgtatttgga--gttcatttgtaatgcgtgactg---actttgtcatgaaacag---------------------------------------------------------

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|58601223|gb|CK011751.1|CK011751
EST:     CTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAG                         TACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
genomic: CTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcac ... tcttatgcagTACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
EST: gi|58659487|gb|CK048167.1|CK048167
EST:     CTGGAGCATTTGGTTGTGGAAAAGCGGTCATTAGTCAGGCACTTTCAAAG                         TACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
genomic: CTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcac ... tcttatgcagTACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
EST: gi|427964|gb|D24110.1|D24110
EST:     CTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAG                         TACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
genomic: CTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcac ... tcttatgcagTACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
EST: gi|27578142|gb|CB000837.1|CB000837
EST:     AAACTGTCATTAGTCAGGCACTTTCAAAG                         TACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
genomic: AAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcac ... tcttatgcagTACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
EST: gi|58594482|gb|CF992790.1|CF992790
EST:     GGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAG                         TACTCCAATTCTGAAGGTGGGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC
genomic: GGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcac ... tcttatgcagTACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAAC

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: 73 (upstream exon), 72 (downstream exon)
Score: 44

TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcac ... tcttatgcagTACTCCAATTCTGAAGCTGTGGTTTATGTGGGCTGCGGGGAAAGAGGAAACGAGATGGCTGAGGTCCTTATGGACTTCCCACAATTGACAATGACATTGC




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTACTTGATGCACTATTTCCCTCAGTTCTTGGAGGAACTTGTGCTATTCCTGGAGCATTTGGTTGTGGAAAAACTGTCATTAGTCAGGCACTTTCAAAGgtattttcactattcctctctatttgataactgctagcattgcccatgggcattagccttttaaaatgactgaattctgtgcctttcctgactgaaaatatcttatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA