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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtgtggttctttgctcgggatttctttgggatattgatggtttcgagttcttgggtttttacggcgatgcctttgcgtgcgctgtatgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAGGATGCTCGGCGAAAGCTAAGGAAATTTCAG

Basic information

species Oryza sativa
transcript LOC_Os01g05510.1
intron # 2
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|58652928|gb|CK041608.1|CK041608
EST:     TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCA                         GTCGGGGAGGAGGAGGAGACAAGGTGGTGCGCGAAGGCTCTTCTGAGCAAG
genomic: TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCAgtgagtgtgg ... atgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
EST: gi|58596595|gb|CK007123.1|CK007123
EST:     TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCA                         GTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
genomic: TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCAgtgagtgtgg ... atgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
EST: gi|88400319|gb|CI591009.1|CI591009
EST:     TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCA                         GTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
genomic: TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCAgtgagtgtgg ... atgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
EST: gi|58689352|gb|CK078039.1|CK078039
EST:     TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCA                         GTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
genomic: TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCAgtgagtgtgg ... atgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
EST: gi|58667230|gb|CK055916.1|CK055916
EST:     TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCA                         GTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
genomic: TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCAgtgagtgtgg ... atgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
EST: gi|117246389|gb|CT843250.1|CT843250
EST:     TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCA                         GTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG
genomic: TGGCGTGGCTGTGCACAAGCGGCGGCGTGGCTTGGCCGTGGAGAACGCCAgtgagtgtgg ... atgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcgagttcttgggtttttacggcgatgcctttgcgtgcgctgtatgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAGGATGCTCGGCGAAAGCTAAGGAAATTTCAG
                                            tatgtata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtgtggttctttgctcgggatttctttgggatattgatggtttcgagttcttgggtttttacggcgatgcctttgcgtgcgctgtatgtatacagGTCGGGGAGGAGGAGGAGACAAGGTGGTGCACGAAGGCTCTTCTGAGCAAGGATGCTCGGCGAAAGCTAAGGAAATTTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA