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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattgcttatgagattcccatagtcccatgtaatccaatgaattgtgtcttgtataatatgaagttctgttccttttaccaagtagaaaaatctg...

Basic information

species Oryza sativa
transcript LOC_Os03g22330.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g22330.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G158662_T01 (Zea mays), 5'ss of exon 3
AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattgctta---tgagattcccatagtcccatgtaatccaatgaattgtgtcttgtataatatgaagttctgttccttttaccaagtagaaaaatctg
||||||||| |  || |||||||||||||||  ||||||||||||||||||||| ||||||||||||||||| || ||||| ||||||||||||||||||||||||   |||    |  | |||  ||         |   ||| || ||||   |   ||| |||| | |   ||     |  |     |||| | |    
AGCAATTCCTTTTGGGTCAACACCCAAGAATAATGATGGCACATCTGATGCTGGAACAAATTGGTTAATGTTTGAGTTGCTGTGGAGAGATTTCTTCAGgtatgtaccacttgccctctgtttcagatgactagccttgtgccattgtattgcaacggatatgatat-aggcaatgcatgctggaaactctagagacaat--

upper sequence: LOC_Os03g22330.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G02240.2 (Glycine max), 5'ss of exon 2
AGCAATTCCATCGGGATCAACACCCAAGA--ATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattgcttatgagatt--cccatagtcccatgtaa---tcca--atgaattgtgtcttgtataatatgaagttctgttccttttaccaagtagaaaaatctg
  || |||      |    |||   | ||   |||| ||||| | ||       |||||||||||||| ||||| || ||||||||||| || ||||| |||||  ||||  || ||   ||      | |       |     | ||  ||  ||| |   ||| || | ||  |      |  |  |   |   ||| |       
-CCATTTCTGCTTCGGCGGACAAGAACGATGGTGGTAATGGCTCGTCCAGAAACGGTACAAATTGGTTGATGTTTGAGTTGCTATGGAGGGACTTCTTTAGgtaaatattttttgtgcacttgttttttggctttgcttggaacttcagtatacatttttctttgcatgagatatatggaaatggcaatggtcctatagca-------
















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|29616243|gb|CB621255.1|CB621255
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|86480762|gb|CI123395.1|CI123395
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88994060|gb|CI116024.1|CI116024
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88250922|gb|CI248773.1|CI248773
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88439604|gb|CI551838.1|CI551838
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88263632|gb|CI367406.1|CI367406
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88445162|gb|CI552215.1|CI552215
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88425028|gb|CI562343.1|CI562343
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|25799829|gb|CA755790.1|CA755790
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|86258820|gb|CI000049.1|CI000049
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|86429391|gb|CI076072.1|CI076072
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|38568777|gb|CD670992.1|CD670992
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|38480046|gb|CF964135.1|CF964135
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88245986|gb|CI245835.1|CI245835
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88228080|gb|CI227560.1|CI227560
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88199863|gb|CI199713.1|CI199713
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|88222823|gb|CI220888.1|CI220888
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|33800287|gb|CF326012.1|CF326012
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|86505349|gb|CI147982.1|CI147982
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|86493833|gb|CI136466.1|CI136466
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
EST: gi|300215532|gb|HO088158.1|HO088158
EST:     GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAG                         GTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC
genomic: GCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCC

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: 59

AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattg ... atatctttagGTTCATCACAAAGAAGTACAGTTCTGCACAGAAGACCTCTGAAGTTGCTCCTGCCACTGGTTGCACCCCTACCCCAGCGCTTGCATAAACTAGATAGTCA




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCAATTCCATCGGGATCAACACCCAAGAATGGTGATGGCACATCTGATGCTGGTACAAATTGGTTAATGTTCGAATTGCTATGGAGAGATTTCTTCAGgtatgtattgcttatgagattcccatagtcccatgtaatccaatgaattgtgtcttgtataatatgaagttctgttccttttaccaagtagaaaaatctg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agaaaaa