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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatagtccatgaggaaatgagttatcttacagaaatatgaacttgcatgtattgcaaacttgtcattttttaatcattcatcaccctctgaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTCAGCTCGCTTTGACTGTTTAAGTCAAGAGTTAAAAAGGATACCCAAGAGT

Basic information

species Oryza sativa
transcript LOC_Os11g44870.1
intron # 2
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|33664522|gb|CF295489.1|CF295489
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACC
EST: gi|87017140|gb|CI286276.1|CI286276
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29667874|gb|CB664149.1|CB664149
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|86890161|gb|CI321338.1|CI321338
EST:     AAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: AAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|86437472|gb|CI119194.1|CI119194
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|86252628|gb|CI003964.1|CI003964
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29658431|gb|CB654706.1|CB654706
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|88227796|gb|CI227276.1|CI227276
EST:     ACGAGTAGGAAGAAATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|86419660|gb|CI054461.1|CI054461
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29638257|gb|CB643266.1|CB643266
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29637810|gb|CB642819.1|CB642819
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|33819603|gb|CF335621.1|CF335621
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|86535609|gb|CI175815.1|CI175815
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29637852|gb|CB642861.1|CB642861
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|86535596|gb|CI175802.1|CI175802
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|89190667|gb|CI392520.1|CI392520
EST:     AGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: AGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|87012785|gb|CI295229.1|CI295229
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29659556|gb|CB655831.1|CB655831
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|87029445|gb|CI250378.1|CI250378
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29660661|gb|CB656936.1|CB656936
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29672236|gb|CB668511.1|CB668511
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|86535610|gb|CI175816.1|CI175816
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|88270242|gb|CI385500.1|CI385500
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|5003516|gb|AU068665.1|AU068665
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|88442248|gb|CI541455.1|CI541455
EST:     TTCAGGTTCCAGAGGTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: TTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29657745|gb|CB654020.1|CB654020
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|29680361|gb|CB676636.1|CB676636
EST:     ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: ACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
EST: gi|88460954|gb|CI553090.1|CI553090
EST:     CTTAAGTCATTCAGGTTCCAGAGCTAG                         ATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC
genomic: CTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTC

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: 70 (upstream exon), 53 (downstream exon)
Score: 27

GTTGCCGATACAGTTGAATCGGTCCATGAGCTCTACACCAGTGAGCGACAACGAGTAGGAAGATATCTAGATGCTTAAGTCATTCAGGTTCCAGAGCTAGgtttgtgcat ... gaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTCAGCTCGCTTTGACTGTTTAAGTCAAGAGTTAAAAAGGATACCCAAGAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcatgtattgcaaacttgtcattttttaatcattcatcaccctctgaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTCAGCTCGCTTTGACTGTTTAAGTCAAGAGTTAAAAAGGATACCCAAGAGT
                       ttttaat  putative branch site (score: 27)
                                       ccctctg  putative PPT
                    attttttaatcattca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatagtccatgaggaaatgagttatcttacagaaatatgaacttgcatgtattgcaaacttgtcattttttaatcattcatcaccctctgaaccttcagATTTATCAATAATCATTATGGAGGTGAAAAGCACCAGCATGACTCAAGTTCAGCTCGCTTTGACTGTTTAAGTCAAGAGTTAAAAAGGATACCCAAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - -gtccatg
- - - - - - - - - - - - - - -acagaaa
- - - - - - - - - - - - - - - - - - - - - - tgcatgt
- - - - - - - - - - - - - - - - - - - - - - - - - - ttgcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cattcat