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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctcttataatctggctttctccaaatttaaggcagttattttatttttgtcgtcattttcagttagtacttgtgatgcatgtcatttttagttt...

Basic information

species Oryza sativa
transcript LOC_Os04g23180.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G032293_T02 (Zea mays), 5'ss of exon 2
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctcttataatctggc-tttctcc--aaatttaaggcagttattttatttttgtcgtcattttcagttagtacttgtgat-gcatgtcatttttagttt-
|| |||||||||||||||||||||||||| ||||||||||| |||||||| ||||||||||| ||||||||||||  ||   ||||| |||||| |||| ||  | || |||  ||||||  | |||||   | ||| |||||||| |||  |||||| ||||| |   || ||    
GTCGTAGATGCTCTTTATGATTGCAAAAGCGAGGTGATTGGGCCAGGATTTTTTAGATTCAAGGCTGAAATTGgt--agtctttatattctggcatttcaccgtatatctaaaacagttacatcatttt---catcactttcagttcgtatctgtgatagcatggccagttgagggca

upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G065839_T01 (Zea mays), 5'ss of exon 10
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctcttataatctggc-tttctccaaat--ttaaggcagttattt-tatttttgtcgtcattttcagttagtacttgtgat-gcatgtc-atttttagttt
||||||||||||||||||||||||||||||||||||||||| ||||| || ||||||||||| ||||||||||||| |    ||||| |||||| |||| ||| ||   |||  |||||| ||  ||  || || |||||| ||||| |||  |||||| ||||||| | |  |     
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGGCCAGGTTTTTTTAGATTCAAGGCTGAAATTGgtatattctttatattctggcatttcaccatatatctaaaacagttagttacatgattttcatcattt-cagttcgtatgtgtgatagcatgtccagtcct-----

upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA07G02280.2 (Glycine max), 5'ss of exon 9
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgt-acagctcttataat-----ctggctttctccaaatttaaggcagttattttatttttgtcgtcattttcagttagtacttgtgatgcatgtcatttttagttt
||||||||| | || ||||||||||||||||| || ||||| || |||||||| ||||| || || ||||| ||| ||   ||| ||  |     ||    ||     |||||| |      || | ||| |     |  | || |  ||  |  |||      |||   |        
GTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAGgttacctttctcatctttgttactattctttgtgtaatttaggttgcgaatataattctgaaatttgtctttatataaaatatgtcccatttgtttgtgc------

upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GLYMA08G23740.2 (Glycine max), 5'ss of exon 10
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctcttataatctggctttctccaaatttaaggcagttattttatttttgtcgtcattt--tcagttagtacttgtgatgcatgtcatttttagttt
||||||||| | || ||||||||||||||||| || ||||| || |||||||| ||||| || || ||||| ||| |   ||| ||        ||  | || | || ||  | | | || ||   ||  |   ||       | | |  |  |||  ||               
GTTGTAGATTCCCTCTATGATTGCAAAAGTGAAGTTATTGGGCCTGGATTCTTCAGATTTAAGGCAGAAATAGgttcctttctcatc------tttgttacagaattcagataatgaatt-atgcatgatggtgttaagctgatcattcttaatgaaacag--------------

upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: AT1G51610.1 (Arabidopsis thaliana), 5'ss of exon 10
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctcttataatctggctttctccaaatttaaggcagttattttatttttgtcgtcattttcagtta---------gtacttgtga-tgcatgtcatttt-tagttt--------------------------------------------------------
||||||||| || | ||||| ||||||||||| |||||||| || |||| ||| ||||| ||||||||||| ||| |   | ||  | | |   |  |||  ||   ||   | || ||   | |   |    ||    ||  |         ||  | | || || |  ||||| | | || |                                                        
GTTGTAGATTCTTTATATGACTGCAAAAGTGAAGTGATTGGTCCTGGATCCTTCAGATTTAAAGCTGAAATAGgtgcgtattttgaactgttattcgctctcaaag-aattgatttgttccctatgcttgaaaataagaaggaaaaaggcaaagtcttagcgagtgaagatcattctatcgtattctgaacttcttgagtgattccattgggcactgtattaattgttgtatttaaacag

upper sequence: LOC_Os04g23180.1 (Oryza sativa), 5'ss of exon 10
lower sequence: Vv09s0054g00220.t01 (Vitis vinifera), 5'ss of exon 10
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgta-cagctcttataatctggctttctccaaattta-aggcagttattttattttt--gtcgtcattttcagttagtacttgtgatgcatgt-catttttagttt
|| || |||||||| |||||||| |||||||||||||||||||| || |||||||| || || || ||||| |||| |   |   | | |      || | || ||||  | |  |||   |||| | |  |||   || |  | | || |  | | |    |   ||    ||    
GTAGTTGATGCTCTATATGATTGTAAAAGTGAGGTGATTGGACCTGGGTTCTTTAGGTTTAAGGCAGAAATAGgtaacctttgccacagtaacttatttttcagatttttatgtggtttggttatctataggtcaatatctcta-tgaggatatctaacatctccacacccata----

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|88490382|gb|CI427654.1|CI427654
EST:     AGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGGATTATTTGGAAAGGACTGGACGTG
genomic: AGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|14713834|gb|AU197796.1|AU197796
EST:     TTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
genomic: TTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|88994589|gb|CI117741.1|CI117741
EST:     CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|8334730|gb|BE039714.1|BE039714
EST:     CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACCGGACGTG
genomic: CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|29613518|gb|CB618531.1|CB618531
EST:     CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|86434642|gb|CI105875.1|CI105875
EST:     CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|4716435|gb|AU057551.1|AU057551
EST:     CAAAANTGAGGTGATTGGACCAGGATTCTTTANATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|9865445|gb|AU101195.1|AU101195
EST:     CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACNTG
genomic: CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|88491764|gb|CI429036.1|CI429036
EST:     GACCAGGATTCTTTAGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGNTGCAGAATTATTTGGAAAGGACTGGACGTG
genomic: GACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
EST: gi|86494278|gb|CI136911.1|CI136911
EST:     CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTG                         ATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG
genomic: CAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTG

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: 43 (upstream exon), 57 (downstream exon)
Score: 8

GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctct ... cttctcatagATTTCAATGGAGTAGTCCTGGTGCAGAATTATTTGGAAAGGACTGGACGTGGAGAATGGGCAAAACAG




<











<


<









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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGTAGATGCTCTTTATGATTGCAAAAGTGAGGTGATTGGACCAGGATTCTTTAGATTCAAAGCTGAAATTGgtacagctcttataatctggctttctccaaatttaaggcagttattttatttttgtcgtcattttcagttagtacttgtgatgcatgtcatttttagttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctttctcc