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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcagtgat...

Basic information

species Oryza sativa
transcript LOC_Os09g26880.3
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os09g26880.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G130440_T01 (Zea mays), 5'ss of exon 3
----ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcagtgat
    || ||||||||| |||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||||| || |||||||||||||| ||   |       | |      ||   || | |||||| |        || |  | | | ||  |   |      || || |||     ||||     
GCAAATCGGTGATGCACTGAGAGCAAAGCTCCATCACCTTGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATCGGTGAGGTTCAGgtaggaatggatcatagttgcttgattgcttctag-tgcattgtctacaaactgcaagtcatgtattgtgc-tcaccaaaagtatcatcattgagttcacgc--

upper sequence: LOC_Os09g26880.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA09G08150.2 (Glycine max), 5'ss of exon 2
----ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaata-ttcagtgat-
    |||||||| |||||||| || ||  |  |||   |||| ||||| ||||| ||||||||||| |||||||| || ||||| ||||| || |||||||||     |||| |     ||||| |||      | | |||   |  |  |||  | || |  | |        ||  ||| |      | |||| |||  |||| 
ACAGATTGGTGAAGCATTGAGGGCCAAATTGGATCCTTTGGGTAGGCTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtat-cgcaatt-ctctttgttctgccatattatgttacatg--tcctgacaccaaagaaatcaga--gtttagattgtgtataaggctataatacttctttgatg

upper sequence: LOC_Os09g26880.3 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA15G19670.1 (Glycine max), 5'ss of exon 3
----ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgccgccagttcttccactcagagcttcattgttttttgcact-caggataggaaatgaccactatattgtgtttctt--cagaatattcagtgat
    |||||||| |||||||| || ||| |  |||   |||| || || ||||| ||||||||||| |||||||| || ||||| ||||| || |||||||||   | ||||    |  ||||| | |||        |||  | |   |     ||| |||| ||        || ||||||| |  |   | || | |       
ACAGATTGGTGAAGCATTGAGGGCCAAGTTGGATCCTTTGGGTAGACTGGTGTCTCTTGAGATGGGAAAAATTCTCCCAGAAGGAATTGGGGAAGTTCAGgtat-cacaattataact-gttctgcaactttttttgacatattatcaggtttgacagcatagaaatcagagtttagattgtgtataatactataacacttc-----

upper sequence: LOC_Os09g26880.3 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv11s0016g00900.t01 (Vitis vinifera), 5'ss of exon 3
----ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcagtgat
    ||||| || ||  | ||||| ||  |       || ||  |||||||||| || |||||||||||||| ||  ||||||| || |||||||||||||||       |      |       | |   |||| || || |||    |   ||   ||  |  ||   |  | | |  ||  |    | ||   ||||    
GCAGATTGGGGAAGCGCTTAGAGCGAAATTGGGGAGTCTTGGTCGGCTTGTGTCGCTGGAGATGGGGAAAATACTGGCTGAAGGAATCGGAGAGGTTCAGgtataacctttcttttactcacaagcgagctagagattgat-gttgagagtgttc--catgaggcattgtccttttgtgctgcattaagacaagcctcaggtg-

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|33676797|gb|CF305036.1|CF305036
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29668655|gb|CB664930.1|CB664930
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29617477|gb|CB622489.1|CB622489
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29656047|gb|CB652322.1|CB652322
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33797257|gb|CF324491.1|CF324491
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29656045|gb|CB652320.1|CB652320
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29668613|gb|CB664888.1|CB664888
EST:     TGAGATGGGGAAAATTCTTCNTGAAGGGATTGGAGACCTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: TGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29638871|gb|CB643880.1|CB643880
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33683878|gb|CF312117.1|CF312117
EST:     CTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: CTTGAGATGGGGAAAATTCTTCCTGAAGGGATT-GGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29665768|gb|CB662043.1|CB662043
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33681819|gb|CF310058.1|CF310058
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29655872|gb|CB652147.1|CB652147
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29661446|gb|CB657721.1|CB657721
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|33675985|gb|CF304224.1|CF304224
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29674834|gb|CB671109.1|CB671109
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|59930146|gb|AB178688.1|AB178688
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGG-A-                         -AA-TCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|58689444|gb|CK078131.1|CK078131
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGG-A-                         -AA-TCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29673252|gb|CB669527.1|CB669527
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29628521|gb|CB633532.1|CB633532
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGG-A-                         -AA-TCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
EST: gi|29677488|gb|CB673763.1|CB673763
EST:     ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTC----AG                         GAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT
genomic: ACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAAT

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), 75 (downstream exon)
Score: 125

ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgc ... tgttttgtagGAAATCATTGACATGTGTGATTATGCTGTGGGCCTAAGTCGCCAGCTAAATGGGTCCATCATACCATCTGAAC




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTGGTGATGCATTGAGAGCAAAGCTCCATCACCTGGGCAGGCTTGTGTCACTTGAGATGGGGAAAATTCTTCCTGAAGGGATTGGAGAGGTTCAGGTAGgtataattgccgccagttcttccactcagagcttcattgttttttgcactcaggataggaaatgaccactatattgtgtttcttcagaatattcagtgat

- - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgccgcc