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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tggtgattttccatccacattataacgtgaatttgtttgcacaatggactttcaggatttaagtgaacaaagtaaccgatttgataatctatacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATTTAGATCCATGTATGCCATTGACAGTAGCAAGTACCCTCATCTAAGGATC

Basic information

species Oryza sativa
transcript LOC_Os11g31700.1
intron # 5
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|88420158|gb|CI513839.1|CI513839
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAAT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGA-Ggtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAAT
EST: gi|88253414|gb|CI352040.1|CI352040
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
EST: gi|88419813|gb|CI513865.1|CI513865
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
EST: gi|12404885|gb|AU166486.1|AU166486
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
EST: gi|88380040|gb|CI513630.1|CI513630
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
EST: gi|88465097|gb|CI514869.1|CI514869
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
EST: gi|88462358|gb|CI514490.1|CI514490
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
EST: gi|88435941|gb|CI514080.1|CI514080
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
EST: gi|88455242|gb|CI516880.1|CI516880
EST:     TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAG                         GTTGANNNNNNNGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT
genomic: TTTATTTTGAGATGATGCAAGAAGTGGATACAATGGTTGGGTGTTTTGAGgtaatttttc ... atacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggactttcaggatttaagtgaacaaagtaaccgatttgataatctatacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATTTAGATCCATGTATGCCATTGACAGTAGCAAGTACCCTCATCTAAGGATC
                                 atttgataatctata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tggtgattttccatccacattataacgtgaatttgtttgcacaatggactttcaggatttaagtgaacaaagtaaccgatttgataatctatacttgcagGTTGATTTTTTTGGACCGGGAAGTTCTATATAAGAAATTGAGGCCTGAATTTAGATCCATGTATGCCATTGACAGTAGCAAGTACCCTCATCTAAGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG