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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagccatctctctcatcgtctcttctttctttcttcattctaattattaagatgttgattaattatgcaaataaatgcttgtgcatatatatatatatgtatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG

Basic information

species Oryza sativa
transcript LOC_Os02g01150.4
intron # 6
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|38477990|gb|CF962123.1|CF962123
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|10794734|gb|AU108700.1|AU108700
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|11442863|gb|BF430762.1|BF430762
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|86906454|gb|CI294577.1|CI294577
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|58605093|gb|CK033126.1|CK033126
EST:     CATGGAAGAGAGCCGCCACCATGGGGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
EST: gi|38481826|gb|CF965897.1|CF965897
EST:     CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTG                         ATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG
genomic: CATGGAAGAGAGCCGCCACCATGGAGGATGTCCTCAGGGAGGCCGACGTGgtcagccatc ... tatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattaattatgcaaataaatgcttgtgcatatatatatatatgtatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG
  gattaat  putative branch site (score: 3)
                              atatatatatatatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagccatctctctcatcgtctcttctttctttcttcattctaattattaagatgttgattaattatgcaaataaatgcttgtgcatatatatatatatgtatgtggcagATTAGTCTGCACCCTGTGTTGGACAAGACCACTTACCATCTGATAAACCCGGAAAGGCTGGCCATCATGAAGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG