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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagcattgtcaagtgcttgtctagtcgaacttaaagttgctgtcatgggataaattgcatgaaaatgtacttttgttgatttcatttttaattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG

Basic information

species Oryza sativa
transcript LOC_Os01g40690.1
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|568850|gb|D39699.1|D39699
EST:     CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTC                         GAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
genomic: CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTCgtccgtacac ... aattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
EST: gi|88421754|gb|CI621398.1|CI621398
EST:     CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTC                         GAAAAACTCCACCAGTGGATATTGAGAAAGCACGAGGAAGAGTCGAGGCTC
genomic: CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTCgtccgtacac ... aattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
EST: gi|32948314|gb|BP184886.1|BP184886
EST:     CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTC                         GAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
genomic: CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTCgtccgtacac ... aattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
EST: gi|218495366|gb|FG958231.1|FG958231
EST:     CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTC                         GAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
genomic: CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTCgtccgtacac ... aattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
EST: gi|218496837|gb|FG946813.1|FG946813
EST:     CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTC                         GAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC
genomic: CCATGGCCCAGCAGAAGCTCTCCTTCCAGGCCGGCGAGCGCCACTCCCTCgtccgtacac ... aattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgggataaattgcatgaaaatgtacttttgttgatttcatttttaattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG
                                         ttttaat  putative branch site (score: 3)
                          ttttgttgatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaagcattgtcaagtgcttgtctagtcgaacttaaagttgctgtcatgggataaattgcatgaaaatgtacttttgttgatttcatttttaattgtgcagGAAAAACTCCACCAGTGGATATTGAGAAAGCATGAGGAAGAGTCGAGGCTCACGGCGGCTGATATAATGTCTCATATCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT