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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggcatggcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT

Basic information

species Oryza sativa
transcript LOC_Os02g52860.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G015401_T01 (Zea mays), 3'ss of exon 3
tggcatggcaccaatga-gtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
     ||| |    |    | | | ||| | |||| || |   ||| ||  | |||| ||||    | ||  || |||| |    | |     || | ||||||| |||||||||||||| |||||||||||||| |||||  | ||||||||||| ||||| ||||||||||||||||||||||||||| ||  ||| ||
-catttggtagttgtattatatatttttatctattcttgttcaagccatattctcatattataagctgtactcacccatcgcccttgtatgatgtatgcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G152827_T01 (Zea mays), 3'ss of exon 3
tggcatggcaccaatga-gtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
     ||| |    |    | | | ||| | |||| |  |   ||| ||  | |||| ||||    |  |  || |||| |    | |     || | ||||||| |||||||||||||| |||||||||||||| |||||  | ||||||||||| ||||| ||||||||||||||||||||||||||| ||  ||| ||
-aatttggtagttgtattatatatttttatctattctcgttcaagccatattctcatattataagctgaactcacccatcgcccttgtatgatgtatgcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATCTACAAGCATGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G060630_T01 (Zea mays), 3'ss of exon 3
tggcatggcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
|    ||| |    |    | |  ||| |||||| | |||  ||| ||  | | |||||||    | ||  || |  ||| |    |     || | ||||||| |||||||||||||| |||||||||||||| |||||  | || |||||||||||||| ||||||||||||||||||||||||||| ||  ||| ||
taatttggtatttgtattatataatttatttattatcatgcaagccatattcttatgttataagctgtactcacctgttgcactcgtatgatgtatgcagATACCATGATGAAGTTTGCTTCCTTTGAGACCATCGTTGAGCTTATATACAAGCACGCTGTGCCTGTTCCGAAGTCTGAGTGCAGCAAGACTACCCAGTT

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G05460.1 (Glycine max), 3'ss of exon 3
---tggcatg-gcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
   ||   |  |   || |    | || |   || || | ||  |  |   || |  |   | || |   || |  | | ||  ||   |||  || ||  |||| || |||||||||||||| || |||||||||||||||||  ||||||| ||||||||  | ||    || |||  |||||||| |||     | ||| |
gtttgaggtctgtttcatttgcatcttataacttgatatata-aaaggtcctgatacctgataatatgacctgtataac-ataaaaatgttctttcttg--cagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTTGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA16G05450.1 (Glycine max), 3'ss of exon 4
---tggcatg-gcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
   ||   |  |   || |    | || |   || || | ||  |  |   || |  |   | || |   || |  | | ||  ||   |||  || ||  |||| || |||||||||||||| || |||||||||||||| ||  ||||||| ||||||||  | ||    || |||  |||||||| |||     | ||| |
gtttgaggtctgtttcatttgcatcttataacttgatatata-aaaggtcctgatacctgataatatgacctgtataac-ataaaaatgttctttcttg--cagACACAATGATGAAGTTTGCTTCGTTTGAGACCATTGTAGAGCTGATCTATAAGCACGCCATCCCAACACCAAAGAATGAGTGCACCAAAGGCCTGCAACT

upper sequence: LOC_Os02g52860.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GLYMA19G27380.1 (Glycine max), 3'ss of exon 3
----tggcatggcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
      || | |   || | |  | || |   || || | ||  |  |   || |  |   | ||     || |    | ||  ||   |||  || ||  |||| || |||||||||||||| || |||||||||||||||||  ||||||| ||||| ||  | ||    || |||  |||||||| |||     | ||| |
gtttgagctttgtttcatttacatcttataacttgatatata-aaaggtcctggtacctgataataaaacctgtatgac-ataaaaatgttctttcttg--cagACACAATGATGAAGTTTGCTTCTTTTGAGACCATTGTTGAGCTGATCTATAAGCATGCCATCCCAACACCAAAGAATGAGTGCACCAAAAGCCTGCAACT

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|116875543|gb|EC366051.1|EC366051
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|163929346|gb|EG713771.1|EG713771
EST:     TCTTGGGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: TCTTGGGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|29628300|gb|CB633311.1|CB633311
EST:     TGGGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: TGGGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|29677044|gb|CB673319.1|CB673319
EST:     GGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GGCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|218484707|gb|FG949606.1|FG949606
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|218490441|gb|FG950234.1|FG950234
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|163928501|gb|EG711386.1|EG711386
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|218505349|gb|FG953708.1|FG953708
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|58680384|gb|CK069071.1|CK069071
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTGTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|66913316|gb|CX100164.1|CX100164
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|29658502|gb|CB654777.1|CB654777
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|116874996|gb|EC365504.1|EC365504
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|11025863|gb|AU162464.1|AU162464
EST:     CTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAAGTTTGCCTCCCTTTGAGNCCATTGTTGAAATGATCTA
genomic: CTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATG-AAGTTTGCCT-CCTTTGAGACCATTGTTGAAATGATCTA
EST: gi|14192020|gb|AU184231.1|AU184231
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|29630080|gb|CB635089.1|CB635089
EST:     AGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: AGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|29630079|gb|CB635088.1|CB635088
EST:     GCTTTACAAGGGAATTGTTCCTCTGAGGGGTCGCCAAATCCCTT                         ATACTATGATGAAG
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAG
EST: gi|29658501|gb|CB654776.1|CB654776
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTTGAA-TGATCTAC
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTT-GAAATGATCTAC
EST: gi|218501146|gb|FG957968.1|FG957968
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|163929256|gb|EG713081.1|EG713081
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|116875503|gb|EC366011.1|EC366011
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
EST: gi|38470606|gb|CF954737.1|CF954737
EST:     GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTT                         ATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA
genomic: GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACA

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), 47 (downstream exon)
Score: 159

GCTTTACAAGGGAATTGTTCCTCTGTGGGGTCGCCAAATCCCTTgtaagtatta ... tcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT
                                       tttccatc  CT-rich tract
                               attgaatattt  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggcatggcaccaatgagtttttgtttgtttatttttatgagagctatgctgtcatgttatttcttctatgcatccattgaatatttccatcgtgtccagATACTATGATGAAGTTTGCCTCCTTTGAGACCATTGTTGAAATGATCTACAAGCACGCTGTTCCTGTTCCGAAGTCTGAGTGCAGCAAGTCTTTCCAATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
-ggcatgg
- - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - -tgctgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatcc