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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgtgatagcacaggtttgagaacattagtgcttattaattatatggaaatatctgttacatattttgcttgctatttattacttgttgtgataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT

Basic information

species Oryza sativa
transcript LOC_Os03g06120.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g06120.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G027821_T01 (Zea mays), 3'ss of exon 4
ctgtgatagcacagGTTTGAGAACATTAGTGCTTATTAATTATATGGAAATATCTGTTACAT-ATTTTGCTTGCTATTTAT-TACTTGTTGTGATAACACAGGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT
      | | || | |   ||   || | || | |        ||||  || |   | |||| |||||| || |  |  || |  ||| | |||||||| ||||||||  || || || |||||||||||||| ||||| |  ||||||||||| || ||| ||||||| ||||
--tcctttgtactgttgccagtttataattggtcaacccaggcatggggattttactaacatgattttgtttccgttgcatgtgtttgctatgataacatagGTTTGAAGACCTTGTTCTTCCCCTGTGGAACCTTCTCGAGAATTGCTTCAATCGCCAAGGACAGGCCAATGT
















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|25806375|gb|CA762336.1|CA762336
EST:     CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|87021652|gb|CI276051.1|CI276051
EST:     CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|58681562|gb|CK070249.1|CK070249
EST:     CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|58673353|gb|CK062039.1|CK062039
EST:     CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|44674180|gb|CR287614.1|CR287614
EST:     GACGAGTAGG-ATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTGTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: GACGAGT-GGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|29637808|gb|CB642817.1|CB642817
EST:     CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|89169017|gb|CI020557.1|CI020557
EST:     TGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: TGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|33803494|gb|CF327622.1|CF327622
EST:     CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
EST: gi|27548516|gb|CA766467.2|CA766467
EST:     CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGT                         GTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA
genomic: CGACGAGTGGCATGCAGATTTGCTTGGTTGCTGTTCAGAGCCATCTTTGTgtatgtccat ... gataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggaaatatctgttacatattttgcttgctatttattacttgttgtgataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT
                                            tgataac  putative branch site (score: 2)
                            tatttattacttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgtgatagcacaggtttgagaacattagtgcttattaattatatggaaatatctgttacatattttgcttgctatttattacttgttgtgataacacagGTTTGAGAACATTCTTTTTCCCCTGTGGAACATTCTCAAAGATTGCTTCAATTGCGAAGAACAGGCCCATGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC