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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatgcccataatatgatatggttatcaggcaatggatagtagcctaggactgcacctagccacatttcttaacagtgatgatttattactatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCATCTGATAGCCCATATGCTGGTGGAGTTTTCCTAGTTACCATCCACTTCCC

Basic information

species Oryza sativa
transcript LOC_Os01g46926.2
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|86849404|gb|CI299631.1|CI299631
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATCATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88729958|gb|CI753573.1|CI753573
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATNATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88294636|gb|CI602356.1|CI602356
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCC-TACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGAAATGTTCCAATGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|86902035|gb|CI300274.1|CI300274
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88745084|gb|CI768444.1|CI768444
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|3759930|gb|C97188.1|C97188
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88346503|gb|CI637349.1|CI637349
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88730304|gb|CI753918.1|CI753918
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88762126|gb|CI771682.1|CI771682
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATNATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|58594773|gb|CF993081.1|CF993081
EST:     GAAGGAGCTCAAGGATCTGCAAAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88718883|gb|CI742393.1|CI742393
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|86898750|gb|CI296063.1|CI296063
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88730675|gb|CI754288.1|CI754288
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATNATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|86898783|gb|CI296080.1|CI296080
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88692482|gb|CI736057.1|CI736057
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATNATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|88570585|gb|CI661958.1|CI661958
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT
EST: gi|87019040|gb|CI297348.1|CI297348
EST:     GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAG                         GTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATNATGGGTCCAT
genomic: GAAGGAGCTCAAGGATCTGCAGAAGGATCCCCCTACATCATGCAGTGCAGgtcttgcttt ... tatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taggactgcacctagccacatttcttaacagtgatgatttattactatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCATCTGATAGCCCATATGCTGGTGGAGTTTTCCTAGTTACCATCCACTTCCC
                      tcttaac  putative branch site (score: 2)
                                 atgatttattactatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatgcccataatatgatatggttatcaggcaatggatagtagcctaggactgcacctagccacatttcttaacagtgatgatttattactatttgacagGTCCTGTTGGTGAAGACATGTTCCACTGGCAGGCAACGATAATGGGTCCATCTGATAGCCCATATGCTGGTGGAGTTTTCCTAGTTACCATCCACTTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG