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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttactctttatgtaaagtagttaagagtgccttaaacaaccaagcggctgtacaaccttttgacacactctcccttttatccttgcaattttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAGCTGCCCGTCGGCCGCGAATTGCGCAAAATGGGCTCAAACCTACCTGAAG

Basic information

species Oryza sativa
transcript LOC_Os01g16170.3
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|29663778|gb|CB660053.1|CB660053
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29677835|gb|CB674110.1|CB674110
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29639705|gb|CB644714.1|CB644714
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29679456|gb|CB675731.1|CB675731
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29630352|gb|CB635361.1|CB635361
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29629095|gb|CB634106.1|CB634106
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29616200|gb|CB621212.1|CB621212
EST:     AAGGGAGAAATTAAAAAATATATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29672767|gb|CB669042.1|CB669042
EST:     TATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: TATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29677585|gb|CB673860.1|CB673860
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|58587497|gb|CF985805.1|CF985805
EST:     AGGGAGAAATTAAAAAGAGAGATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AGGGAGAAATTAAAAA-AAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29681319|gb|CB677594.1|CB677594
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|58657684|gb|CK046364.1|CK046364
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29624849|gb|CB629860.1|CB629860
EST:     TATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: TATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29641024|gb|CB646031.1|CB646031
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29678251|gb|CB674526.1|CB674526
EST:     TATATACAGCGAGAGATTTTTCTCTCTCCG                         GTCGGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
genomic: TATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG
EST: gi|29664792|gb|CB661067.1|CB661067
EST:     AAGGGAGAAATTNNNNNNNNTATATACAGTGAGAGATTTTTCTCTCTCCG                         GTCTGGAGCACAAATGGGCATCTTTAGTGGAGCGGGAGCACATCGCCCTAG
genomic: AAGGGAGAAATTAAAAAAAATATATACAGTGAGAGATTTTTCTCTCTCCGgtacgaaccc ... tttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cggctgtacaaccttttgacacactctcccttttatccttgcaattttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAGCTGCCCGTCGGCCGCGAATTGCGCAAAATGGGCTCAAACCTACCTGAAG
             ttttgac  putative branch site (score: 3)
                                            ttttgcttc  putative PPT
                              ttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttactctttatgtaaagtagttaagagtgccttaaacaaccaagcggctgtacaaccttttgacacactctcccttttatccttgcaattttgcttcagGTCTGGAGCACAAATGGGCATCTTCAGTGGAGCGGGAGCACATCGCCCTAGCTGCCCGTCGGCCGCGAATTGCGCAAAATGGGCTCAAACCTACCTGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG