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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...caaatcttcagtgacttgatatggtaacttgctgatgttattctacttatgtttttgttgtgtagatgtaacaaattctatattcaattttgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTGGCAAGTACACCTGGTGATGCTGGTGCAGATAACTTAAAGACTAAGAAGA

Basic information

species Oryza sativa
transcript LOC_Os07g12830.1
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|88363087|gb|CI616244.1|CI616244
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
EST: gi|2309695|gb|C25850.1|C25850
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCANCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTN
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
EST: gi|88578685|gb|CI687630.1|CI687630
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCC
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCC
EST: gi|88393825|gb|CI621320.1|CI621320
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTACAGCTATCCCTGTG
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
EST: gi|58693203|gb|CK081890.1|CK081890
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
EST: gi|58602896|gb|CK013424.1|CK013424
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
EST: gi|88333341|gb|CI642378.1|CI642378
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
EST: gi|86902703|gb|CI306506.1|CI306506
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCC
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCC
EST: gi|88308859|gb|CI654142.1|CI654142
EST:     GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAG                         ATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG
genomic: GCGGATTCGCGATGGCGGATGAAGAGTCGTCTGACTTCACCTTTTGCAAGgttttattta ... tgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatgtttttgttgtgtagatgtaacaaattctatattcaattttgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTGGCAAGTACACCTGGTGATGCTGGTGCAGATAACTTAAAGACTAAGAAGA
                    atgtaac  putative branch site (score: 3)
                                          ttttgttttct  putative PPT
                       taacaaattctatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
caaatcttcagtgacttgatatggtaacttgctgatgttattctacttatgtttttgttgtgtagatgtaacaaattctatattcaattttgttttctagATCGATTTTGAGGGAGATGGTGGTCTGGAGTTCCCTAAAGCTATCCCTGTGGCAAGTACACCTGGTGATGCTGGTGCAGATAACTTAAAGACTAAGAAGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG