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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatggttgctatctgccagtacaaatctgattctgagatggatttcgttccaacttccaaagcttatcttatttttggtccatgattttgcagagcagTTGGGAAGGGAACAACAAGTAGACGTCGTCTTCGTCTTCTTCAAGGAGAAGCCGATGACTCTGCGGCCACTCAACACAGAGAGAAGCTTCCTCCTCTCCT

Basic information

species Oryza sativa
transcript LOC_Os01g38980.1
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|88410039|gb|CI573278.1|CI573278
EST:     CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAGCCG                         TTGGGAAGGGAACAACAAGTAGACGTCGTCTTCGTCTTCTTCAAGGAGAAG
genomic: CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAGCCGgtatgcacta ... tgcagagcagTTGGGAAGGGAACAACAAGTAGACGTCGTCTTCGTCTTCTTCAAGGAGAAG
EST: gi|88325807|gb|CI649642.1|CI649642
EST:     CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAGCCGAGCAG                     
genomic: CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAG-C---C-Ggtatgcacta ... tgcaga
EST: gi|88318151|gb|CI629432.1|CI629432
EST:     CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAGCCGAGCAG                     
genomic: CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAG-C---C-Ggtatgcacta ... tgcaga
EST: gi|88368498|gb|CI572707.1|CI572707
EST:     CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAGCCGAGCAG                     
genomic: CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAG-C---C-Ggtatgcacta ... tgcaga
EST: gi|88386832|gb|CI629159.1|CI629159
EST:     CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAGCCGAGCAG                     
genomic: CTTCTCCTTCATCATCTTCCTCTATTCATCGCCGCCGCCGAGCTCAG-C---C-Ggtatgcacta ... tgcaga


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcgttccaacttccaaagcttatcttatttttggtccatgattttgcagagcagTTGGGAAGGGAACAACAAGTAGACGTCGTCTTCGTCTTCTTCAAGGAGAAGCCGATGACTCTGCGGCCACTCAACACAGAGAGAAGCTTCCTCCTCTCCT
                    ttatcttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatggttgctatctgccagtacaaatctgattctgagatggatttcgttccaacttccaaagcttatcttatttttggtccatgattttgcagagcagTTGGGAAGGGAACAACAAGTAGACGTCGTCTTCGTCTTCTTCAAGGAGAAGCCGATGACTCTGCGGCCACTCAACACAGAGAGAAGCTTCCTCCTCTCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - tggttgc
- - - - - - - ctgccag
- - - - - - - - - - - - - - ctgattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtccatg