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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa...

Basic information

species Oryza sativa
transcript LOC_Os06g02380.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G065023_T01 (Zea mays), 5'ss of exon 3
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatg-gttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa
|||||| |||||||  |||| ||| ||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| || ||||||||||| ||||| ||   | |   | | | ||  | | | ||| |   |  |  |     ||| | |     |  |     |  ||   |||  || ||            
AAAGGTTGTCCTTACGAAAGGGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgttt--ttatgaacctaatttgcag-----------

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G095252_T02 (Zea mays), 5'ss of exon 2
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa
|||||| |||||||  |||||||| ||||||||||||||||||||||| || ||||| ||||| ||||||||||||||||| || ||||||||||| ||||| | | |  | |   |    |  ||   ||  | | ||  | |  | ||  |     | |       ||   || || ||   || |||   | |||| 
AAAGGTTGTCCTTACTAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGACGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctctgaccttttcctgttctctttg--ttcactcgattttactgctcaggtgaaaatct-----gaaagtctgctttta---tcaacctaatttttag

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G083716_T04 (Zea mays), 5'ss of exon 7
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatg-gttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa
|||||| |||||||  |||||||| ||||||||||||||||||||||| || ||||||||||| ||||||||||||||||| || ||||||||||| ||||| ||   | |   | | | ||  | | | ||| |   |  |  |     ||| | |     |  |     |  ||   |||  || ||            
AAAGGTTGTCCTTACGAAAGAGTCGACAACAATTGTTGGTGATGGCAGCACCCAGGAAGAAGTTACTAAGAGGGTTGCACAGATTAAAAATCTCATTGAGgtctgaccttttcctgttctatttgctcacttgactttactgctcaggtgaaagtctgaagctctgttt--ttatgaacctaatttgcag-----------

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA08G18760.2 (Glycine max), 5'ss of exon 7
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtg-gttctatattccaccatt-tctttaa---
 |||||||| || | ||| ||  |||| ||||||||||||||||| ||||| ||||||| |||||  ||||| ||||||||||| |  || || || ||||| ||||   ||| |    |        | |  | |  |    || |  |||| |||     ||  |   | |   || |    || ||| |   | ||| |   
CAAGGTGGTGCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAAATTAGGAACCTAATTGAGgt-tgttccttctctccctccccccccctctctctctgt----ccaccaaaatgtttgcacatgcaaatgtggcatgtgcggggtttcacgaagatatttcacat

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA15G40110.1 (Glycine max), 5'ss of exon 7
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa----
 |||||||| || | ||| ||  |||| ||||||||||||||||| ||||| ||||||| |||||  ||||| |||||||| || |  || || || ||||| | ||  |||| | |    |  |   |       |||  |  | |    |    |    | ||||   |         ||||| |||        | |    
CAAGGTGGTTCTCACCAAGGATACAACCACAATTGTTGGTGATGGAAGTACCCAGGAAGCAGTGAACAAGAGAGTTGCACAGATTAGGAACCTAATTGAGgtct-ttccatctctctctttt--tctctccactgaaatgtttgcacatgcaaacgtggcatgggca-ggtttcatgaagatatttcacagaaaacatgactga

upper sequence: LOC_Os06g02380.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv09s0002g03930.t01 (Vitis vinifera), 5'ss of exon 7
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa
 || ||||| || | ||| ||  |||| ||||||||||||||||||||||||||||||| ||| | |||| | ||||| || || | ||| ||  | |||||     |||||| | ||      ||  || | |    || ||  | || | | | || |  |||    ||     | |                     
TAAAGTGGTGCTCACCAAGGATACAACTACAATTGTTGGTGATGGCAGTACACAGGAAGCAGTAAATAAGCGAGTTGCGCAGATCAGAAACCTTGTTGAGgtg---catatctatatagt-cacttttttcgactgtctattgtgttgctagtctcttgtgatggatgtatgaatatgcag-------------------

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|29627635|gb|CB632646.1|CB632646
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|7212768|gb|D46006.2|D46006
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|6934900|gb|AU082437.1|AU082437
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|29618035|gb|CB623047.1|CB623047
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|29624254|gb|CB629265.1|CB629265
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|87011216|gb|CI287893.1|CI287893
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|29616041|gb|CB621053.1|CB621053
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|218493375|gb|FG949729.1|FG949729
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|58687616|gb|CK076303.1|CK076303
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAA
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAA
EST: gi|58690567|gb|CK079254.1|CK079254
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
EST: gi|58602788|gb|CK013316.1|CK013316
EST:     CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAG                         GCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG
genomic: CACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAG

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), 75 (downstream exon)
Score: 216

AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttata ... caatttgcagGCTGCCGAACAAGAATACGAGAAGGAAAAGCTCAATGAGAGGATTGCAAAGCTTGCTGGTGGTGTTGCAGTCATTCAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGGTGGTCCTTAACAAAGAGTCAACAACAATTGTTGGTGATGGCAGTACACAGGAAGAAGTGACTAAGAGGGTTGCACAAATAAAAAATCTCATCGAGgtatgttatatctgtttaccatggttaatttggcacaatagtgcctcgcaaatttttttttttggcacaatagtggttctatattccaccatttctttaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG