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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattaacagtaatagatttagctgcaagctaatggcaacagtaatcatgcaatgcagtctacttatttcatatatgttaatggcgtcatttttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCAATGTCAAAGAGGATGGACAGGAACAAGTGGATCATTGGGGGGATAATTG

Basic information

species Oryza sativa
transcript LOC_Os01g51120.1
intron # 4
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|86821379|gb|CI266822.1|CI266822
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|86824849|gb|CI265057.1|CI265057
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|86544965|gb|CI185171.1|CI185171
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|86600475|gb|CI356232.1|CI356232
EST:     GGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATAGTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: GGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|89190515|gb|CI015480.1|CI015480
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|88200363|gb|CI200213.1|CI200213
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|86543538|gb|CI183744.1|CI183744
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|300215677|gb|HO088303.1|HO088303
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGNGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|16577712|gb|BI811807.1|BI811807
EST:     TTCAGGATCTTCATCAACAAC-GCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCACAGAGTAAAAAGATCCTGGCGGC
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCA-AGAGTAAAAAGATCCTGGCGGC
EST: gi|86825862|gb|CI362342.1|CI362342
EST:     TCAGGATCTTCATCAACAACGGCAAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TCAGGATCTTCATCAACAACGGC-AGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|10611250|gb|AU108201.1|AU108201
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|29660224|gb|CB656499.1|CB656499
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|31818571|gb|CD645560.1|CD645560
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|88530200|gb|CI458577.1|CI458577
EST:     ATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: ATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|88297966|gb|CI555981.1|CI555981
EST:     ATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: ATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|44672388|gb|CR285822.1|CR285822
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|88212113|gb|CI211753.1|CI211753
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|86535676|gb|CI175882.1|CI175882
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|33686215|gb|CF314454.1|CF314454
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|86541601|gb|CI181807.1|CI181807
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|88204477|gb|CI204326.1|CI204326
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|88458512|gb|CI550052.1|CI550052
EST:     AGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: AGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|86257527|gb|CI004344.1|CI004344
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|88215229|gb|CI215078.1|CI215078
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
EST: gi|44678637|gb|CR292071.1|CR292071
EST:     TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACT                         TTGCATGGGATTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA
genomic: TTCAGGATCTTCATCAACAACGGCAGTCACTGCTGCACGCTCATACTACTgtacgtattc ... tttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcaatgcagtctacttatttcatatatgttaatggcgtcatttttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCAATGTCAAAGAGGATGGACAGGAACAAGTGGATCATTGGGGGGATAATTG
                             tgttaat  putative branch site (score: 3)
                                        tcatttttctc  putative PPT
              tacttatttcatatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattaacagtaatagatttagctgcaagctaatggcaacagtaatcatgcaatgcagtctacttatttcatatatgttaatggcgtcatttttctcacagTTGCATGGGGTTGATGATAATGTTGGCAAGAGTAAAAAGATCCTGGCGGCAATGTCAAAGAGGATGGACAGGAACAAGTGGATCATTGGGGGGATAATTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA