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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgtccttggtgagtacttgcctgcaattatatgaaaccaataggatcagatatcgctatattcatgcttgtgaaacaagaaatggtcttattgttttgactttttccaaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g37910.3
intron # 3
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|58692544|gb|CK081231.1|CK081231
EST:     TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTG                         GTGTCCTTGGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAG
genomic: TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGgtgtccttgg ... aaaatttcagG-G--------ATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAG
EST: gi|4715544|gb|AU056660.1|AU056660
EST:     TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                 
genomic: TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCAT---GG----GG-GTCC-TGgtgtccttgg ... aa
EST: gi|163923567|gb|EG713308.1|EG713308
EST:     TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                 
genomic: TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCAT---GG----GG-GTCC-TGgtgtccttgg ... aa
EST: gi|58692937|gb|CK081624.1|CK081624
EST:     TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                 
genomic: TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCAT---GG----GG-GTCC-TGgtgtccttgg ... aa
EST: gi|33799061|gb|CF325390.1|CF325390
EST:     TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTG                         GTGTCCTTGGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAG
genomic: TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGgtgtccttgg ... aaaatttcagG-G--------ATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAG
EST: gi|58691202|gb|CK079889.1|CK079889
EST:     TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                 
genomic: TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCAT---GG----GG-GTCC-TGgtgtccttgg ... aa
EST: gi|58688098|gb|CK076785.1|CK076785
EST:     TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCATGGGGGTCCTGGTGTCCTTG                 
genomic: TGGCCCCAACGATCATATTTTCATTTTTTACAGTGACCAT---GG----GG-GTCC-TGgtgtccttgg ... aa


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgcttgtgaaacaagaaatggtcttattgttttgactttttccaaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG
                               ttttgac  putative branch site (score: 3)
                                     ctttttcca  CT-rich tract
                                      tttttccaaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgtccttggtgagtacttgcctgcaattatatgaaaccaataggatcagatatcgctatattcatgcttgtgaaacaagaaatggtcttattgttttgactttttccaaaatttcagGGATGCCAACCTATCCATACCTCTACGGTGATGATCTTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT