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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcagattagttatttggctattctgcactatataattgctgctgcttgtagttgtagaattgatttgatgaatctgttatctcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTGCCAAATGGCATCAATGTTTATGCCACCACTGCATCAAACGCTGATGAGA

Basic information

species Oryza sativa
transcript LOC_Os01g37910.2
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|58610712|gb|CK038424.1|CK038424
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58677828|gb|CK066515.1|CK066515
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58607687|gb|CK035720.1|CK035720
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58691139|gb|CK079826.1|CK079826
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|4715544|gb|AU056660.1|AU056660
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58691427|gb|CK080114.1|CK080114
EST:     CTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: CTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58600420|gb|CK010948.1|CK010948
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCT
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCT
EST: gi|58692937|gb|CK081624.1|CK081624
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58688098|gb|CK076785.1|CK076785
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58691202|gb|CK079889.1|CK079889
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|163923567|gb|EG713308.1|EG713308
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58690742|gb|CK079429.1|CK079429
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58591094|gb|CF989402.1|CF989402
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58686800|gb|CK075487.1|CK075487
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
EST: gi|58692544|gb|CK081231.1|CK081231
EST:     TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTG                         GTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG
genomic: TTGTAGATGTTCTGAAGAAGAAGCATGCTGCTGGGACGTACAAAAGCCTGgtatcagatt ... tcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgctgcttgtagttgtagaattgatttgatgaatctgttatctcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTGCCAAATGGCATCAATGTTTATGCCACCACTGCATCAAACGCTGATGAGA
                                    tctgttatctccttt  CT-rich tract
                     aattgattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcagattagttatttggctattctgcactatataattgctgctgcttgtagttgtagaattgatttgatgaatctgttatctcctttgcagGTCTTTTACCTTGAAGCCTGTGAATCTGGAAGCATCTTTGAGGGTCTATTGCCAAATGGCATCAATGTTTATGCCACCACTGCATCAAACGCTGATGAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT