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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcagatgttggttatcggatttggtattttaaaatctggtttctgtttggtggatgattgaactgatgtatattgatgtactatttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCTCAGTTAATGATTTCACATGCAAAGTCCAGCAAG

Basic information

species Oryza sativa
transcript LOC_Os12g07450.3
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|29670875|gb|CB667150.1|CB667150
EST:     GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAA                         TGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
genomic: GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAAgtgagcagat ... ttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
EST: gi|29665681|gb|CB661956.1|CB661956
EST:     AATCTTTAGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAA                         TGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
genomic: AATCTTT-GTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAAgtgagcagat ... ttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
EST: gi|33687920|gb|CF316159.1|CF316159
EST:     GAATCTNTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAA                         TGCAAAGATGGAAACACTGAGTGTACATTCCCA
genomic: GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAAgtgagcagat ... ttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCA
EST: gi|58684188|gb|CK072875.1|CK072875
EST:     GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAA                         TGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
genomic: GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAAgtgagcagat ... ttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
EST: gi|66927819|gb|CX114667.1|CX114667
EST:     GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAA                         TGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
genomic: GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAAgtgagcagat ... ttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
EST: gi|218478110|gb|FG955323.1|FG955323
EST:     GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAA                         TGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
genomic: GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAAgtgagcagat ... ttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
EST: gi|58685449|gb|CK074136.1|CK074136
EST:     GAATC-TTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAA                         TGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT
genomic: GAATCTTTGTTGTTAGCCATTCTGATGGAAATCTGTATGTGTACGATAAAgtgagcagat ... ttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtttggtggatgattgaactgatgtatattgatgtactatttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCTCAGTTAATGATTTCACATGCAAAGTCCAGCAAG
                               tattgat  putative branch site (score: 3)
                             tatattgatgtactat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcagatgttggttatcggatttggtattttaaaatctggtttctgtttggtggatgattgaactgatgtatattgatgtactatttatattcagTGCAAAGATGGAAACACTGAGTGTACATTCCCAGCTATAAAGGATCCGGCTCAGTTAATGATTTCACATGCAAAGTCCAGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG