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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caacctctttggaattactcggctaaaggaagaaagaaatgaaatggcaatacagtggggcacacttgtgacgtgtaacatgttctcttttctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG

Basic information

species Oryza sativa
transcript LOC_Os06g36560.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G126900_T01 (Zea mays), 3'ss of exon 2
caacctctttggaattactcggctaaaggaagaaagaaatgaaatggcaatacagtggggcacacttgtgacgtgtaacatgttctcttttctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG
     |     | | | || |  |    |             | || | || ||   |    | |        | |||  |       | || |||||||| |||||||||||||||||||| || ||||| ||||||||||| |||||| | |||||||
--gtatggcctgcactgcttgcttgcttg----------cttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCG

upper sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G126900_T03 (Zea mays), 3'ss of exon 3
caacctctttggaattactcggctaaaggaagaaagaaatgaaatggcaatacagtggggcacacttgtgacgtgtaacatgttctcttttctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG----------------------------------------
     |     | | | || |  |    |             | || | || ||   |    | |        | |||  |       | || |||||||| |||||||||||||||||||| || ||||| ||||||||||| |||||| | |||||||                                        
--gtatggcctgcactgcttgcttgcttg----------cttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAGCAAGGGGAAATCTTGGCGATGCAATATAATACTCA
















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|29644701|gb|CB649708.1|CB649708
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29660840|gb|CB657115.1|CB657115
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|58587863|gb|CF986171.1|CF986171
EST:     AAGGATTTCCCCGACGAGGACTGGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: AAGGATTTCCCCGACGAGGACT-GGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29661872|gb|CB658147.1|CB658147
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29656267|gb|CB652542.1|CB652542
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29676120|gb|CB672395.1|CB672395
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29656245|gb|CB652520.1|CB652520
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|38475187|gb|CF959320.1|CF959320
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGGCA-GGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCAC
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGG-CAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCAC
EST: gi|29680345|gb|CB676620.1|CB676620
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29657369|gb|CB653644.1|CB653644
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29642558|gb|CB647565.1|CB647565
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29669886|gb|CB666161.1|CB666161
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29639892|gb|CB644901.1|CB644901
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|66920340|gb|CX107188.1|CX107188
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29658930|gb|CB655205.1|CB655205
EST:     CCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|87009635|gb|CI309156.1|CI309156
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
EST: gi|29659887|gb|CB656162.1|CB656162
EST:     CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACG                         ATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT
genomic: CAAGGATTTCCCCGACGAGGACTGGCTCCACCTCACTGGCCTCATCCACGgtaaattaaa ... tctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggcaatacagtggggcacacttgtgacgtgtaacatgttctcttttctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG
                           gtgtaac  putative branch site (score: 3)
                                 catgttctcttttctt  CT-rich tract
                                          ttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caacctctttggaattactcggctaaaggaagaaagaaatgaaatggcaatacagtggggcacacttgtgacgtgtaacatgttctcttttctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT