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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcatttcaacttgaaaactatgaacttcaaaatttgtaagctgattgaagcatatatttgaccaaagaaaaaatgtgtattctactgtgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAGGGTGAAGGACTGGTTTACCTTCAATGAGCCGAGATGCGTTGCTGCTCTA

Basic information

species Oryza sativa
transcript LOC_Os07g46280.3
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g46280.3 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G148176_T01 (Zea mays), 3'ss of exon 5
gtaagcatttcaa-cttgaaaactatgaacttcaaaatttgtaagctgattgaagcatatatttgaccaaagaaa--aaatgtgtattctactg---tgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAGGGTGAAGGACTGGTTTACCTTCAATGAGCCGAGATGCGTTGCTGCTCTA
||||| ||| ||| || ||  ||    |    | ||||||  ||  ||||| || ||| | |  | |      |   |  ||       | |      |||| |||||||||||||||||||| || |||||||||||  |||||||||||||||||||| |||||||||||||||| |||||||| ||||| |||||||| 
gtaagaattgcaaactagacgacatctagaaaccaaattt-caaattgattcaaccatgtgtcagtcagtctgacccagctgcacgccgtgcccaatcgaagGGAGGCGTTTGCAGACTACGCCGAGTTCTGCTTCCACGCGTTCGGAGACAGGGTGAAGAACTGGTTTACCTTCAACGAGCCGAGGTGCGTCGCTGCTCTG
















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|29642035|gb|CB647042.1|CB647042
EST:     CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCAAACATCGT                         AGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAG
genomic: CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCAAACATCGTgtaagcattt ... tactgtgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAG
EST: gi|29664412|gb|CB660687.1|CB660687
EST:     CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCAAACATCGT                         AGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAG
genomic: CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCAAACATCGTgtaagcattt ... tactgtgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAG
EST: gi|58673231|gb|CK061917.1|CK061917
EST:     CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCAAACATCGT                         AGAGGCGTTTGCAGACTACGCAGATTTCTGCTTC
genomic: CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCAAACATCGTgtaagcattt ... tactgtgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTC
EST: gi|44664928|gb|CR278362.1|CR278362
EST:     CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCCAACATCGT                         AGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAG
genomic: CCATTAGCACTCCATGAGCAGTACTTAGGCTGGCTAAGCCCAAACATCGTgtaagcattt ... tactgtgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagctgattgaagcatatatttgaccaaagaaaaaatgtgtattctactgtgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAGGGTGAAGGACTGGTTTACCTTCAATGAGCCGAGATGCGTTGCTGCTCTA
                  atttgac  putative branch site (score: 4)
                                          ttctact  putative PPT
                              aaaaaatgtgtatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcatttcaacttgaaaactatgaacttcaaaatttgtaagctgattgaagcatatatttgaccaaagaaaaaatgtgtattctactgtgaagAGAGGCGTTTGCAGACTACGCAGATTTCTGCTTCCAGACGTTCGGAGACAGGGTGAAGGACTGGTTTACCTTCAATGAGCCGAGATGCGTTGCTGCTCTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT