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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgacatattggaatattgaag

Basic information

species Oryza sativa
transcript LOC_Os05g38370.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g38370.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G035922_T02 (Zea mays), 5'ss of exon 2
AGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgc-tgatatggagtgacatatt-ggaatattgaag
||||||||| ||||| |||||||| |||||||||||||||||||||||||| ||||| |||||||| ||||||||||||||||| |||||||||||||||||||        | ||   ||    ||  |||| | ||   ||||||     | ||  ||| ||||  || |||||    || | | |||
AGTTTTCGATACCACCCATGAAGATAACTCTATTTTCTCATTTGAAATTGGACAAGGCGCTGTCATCAAAGCATGGGATATAGCCTTAAGAACTATGAAGgtatg-------tcaacgtttgcgtct--ctcgctttggc-ctttcaccatctctgtgtgacatggtctggcatatccaaaaaaattaag
















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|58653405|gb|CK042085.1|CK042085
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGT
EST: gi|25044727|gb|AJ420710.1|AJ420710
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88209738|gb|CI209587.1|CI209587
EST:     GAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|14571477|gb|BI118845.1|BI118845
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAA-TAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88836064|gb|CI371169.1|CI371169
EST:     GCCAAGGAGCTCTCATTAAAGCAT-GGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACCCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|38477260|gb|CF961393.1|CF961393
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|58670906|gb|CK059592.1|CK059592
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|58676992|gb|CK065679.1|CK065679
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88980703|gb|CI022414.1|CI022414
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGCAAAAATAACATGCAAGCCAGAATACGCATACGGAAGT
EST: gi|88572905|gb|CI664476.1|CI664476
EST:     GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAG                         GTTGGTGAAGTTGC
genomic: GGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaact ... aatattgaagGTTGGTGAAGTTGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGTTTTCGACACCACTCATGAAGACAACTCTATTTTCTCATTTGAAATTGGGCAAGGAGCTGTCATTAAAGCATGGGATATAGCTTTAAGAACTATGAAGgtataaaacttctaaattcttattgctagctcgttctgattctttcaaagattttgctgatatggagtgacatattggaatattgaag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC