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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaccgaccgatcccctctagtctaatcccgatatgccatcgagatcttacgcggaggagtttcccccttttcttggagtacgactaatcgggtgtccgatttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG

Basic information

species Oryza sativa
transcript LOC_Os01g51120.1
intron # 1
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|88741807|gb|CI765315.1|CI765315
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88347779|gb|CI655132.1|CI655132
EST:     TCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCCTC-GCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCT
genomic: TCCGCCTCCCTCTTCCGCAAGTGCACCACCGCC-TCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCT
EST: gi|88329815|gb|CI651484.1|CI651484
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGG
EST: gi|33688115|gb|CF316354.1|CF316354
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88327426|gb|CI645213.1|CI645213
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88361679|gb|CI680250.1|CI680250
EST:     TCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCCTC-GCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: TCCGCCTCCCTCTTCCGCAAGTGCACCACCGCC-TCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|58659193|gb|CK047873.1|CK047873
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88391773|gb|CI603292.1|CI603292
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|300215677|gb|HO088303.1|HO088303
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88342360|gb|CI645882.1|CI645882
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|38482125|gb|CF966182.1|CF966182
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAACAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88569566|gb|CI660741.1|CI660741
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|33686214|gb|CF314453.1|CF314453
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88762529|gb|CI772085.1|CI772085
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88743018|gb|CI766526.1|CI766526
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|33818794|gb|CF335221.1|CF335221
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGTAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88739164|gb|CI762672.1|CI762672
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|88305360|gb|CI653089.1|CI653089
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|163928311|gb|EG712591.1|EG712591
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCG
EST: gi|88765477|gb|CI774571.1|CI774571
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
EST: gi|218478895|gb|FG959664.1|FG959664
EST:     GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAG                         AGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG
genomic: GTCCGCCTCCCTCTTCCGCAAGTGCACCACCGCCTCCGCCCTCGATGGAGgtaaccgacc ... atttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaggagtttcccccttttcttggagtacgactaatcgggtgtccgatttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG
                            gactaat  putative branch site (score: 2)
                                              tttctgc  putative PPT
              ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaccgaccgatcccctctagtctaatcccgatatgccatcgagatcttacgcggaggagtttcccccttttcttggagtacgactaatcgggtgtccgatttctgcagAGAAAAAGAAGCAGAAGCTGTCCGAGATTCAGTCCGGCGTGGAGGAGGCTGAGTCGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG