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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtgtgtgtgtttataatatatttgttggttaactagtctgaatatgccatcgttaggtatgtatacacaatgaactaacatgatgcttgggatttacaacactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGAATGGGCAAGAAATGACACTGCAGCCTTCACTGTAATGTAAGATGTATTA

Basic information

species Oryza sativa
transcript LOC_Os01g31360.2
intron # 9
splice site 3'
intron type U2

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|86539311|gb|CI179517.1|CI179517
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|86539318|gb|CI179524.1|CI179524
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88436264|gb|CI519183.1|CI519183
EST:     ACCTGCAAAAGAAGAGATCGAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|86539310|gb|CI179516.1|CI179516
EST:     GCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: GCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|86539319|gb|CI179525.1|CI179525
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88220009|gb|CI219569.1|CI219569
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88476574|gb|CI413845.1|CI413845
EST:     ACCGGCAAAAGAAGAGATCGAATCCTCAACTCCATTGCCGACTGNACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88319240|gb|CI515701.1|CI515701
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88690409|gb|CI734488.1|CI734488
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88286001|gb|CI515125.1|CI515125
EST:     ATCAAATCCTCAACTCCATTGCCAAGTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|86859907|gb|CI321900.1|CI321900
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88417785|gb|CI535944.1|CI535944
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88691280|gb|CI733864.1|CI733864
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88975210|gb|CI023461.1|CI023461
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88690514|gb|CI734593.1|CI734593
EST:     ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: ACCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
EST: gi|88319314|gb|CI515775.1|CI515775
EST:     CCTGCGAAAGAAGAGATCGAATCCTCAACTCCATTGCCAACTGAACCTG                         ATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA
genomic: CCTGCAAAAGAAGAGATCAAATCCTCAACTCCATTGCCAACTGAACCTGgtgtgtgtgt ... cactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggtatgtatacacaatgaactaacatgatgcttgggatttacaacactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGAATGGGCAAGAAATGACACTGCAGCCTTCACTGTAATGTAAGATGTATTA
                  aactaac  putative branch site (score: 1)
                                     atttacaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtgtgtgtgtttataatatatttgttggttaactagtctgaatatgccatcgttaggtatgtatacacaatgaactaacatgatgcttgggatttacaacactgtgcagATTCGAAGATTCCTACAGACGCACCTGGGGGACCATCAGAAAATCACCAGAATGGGCAAGAAATGACACTGCAGCCTTCACTGTAATGTAAGATGTATTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG