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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacggattttcagtgtagtaaacgaactataatattgtaatacatggggcaataataacaaatactaactgttgttccaactttttgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATCTTTGACTCATTTTGAGAATTGCTTGATACCTGAAGACATCCATGCCAAA

Basic information

species Oryza sativa
transcript LOC_Os03g13790.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G152319_T02 (Zea mays), 3'ss of exon 10
gtacggattttcagtg-tagtaaacgaactataatattgtaatacatggggcaataataacaaatactaactgttgttccaactttttgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATCTTTGACTCATTTTGAGAATTGCTTGATACCTGAAGACATCCATGCCAAA
|||   | ||||  || | |  |   |     ||  |  |    ||   |   ||    |   || |||| | ||||  |||| ||||||   |||||||||||||||||||||||| |||||||| |||||| |||||||| |||||||| || ||||||||  ||||| ||| ||| |||| |||||| | ||||
gtatataatttctctgatcgatagaaagtcgcaacctaatgggtcagttgtagatgcataatgatgctaatt-ttgtgtcaacattttgttgttaagGTATGGTTGGTTTTCCCTTGTTGAGCTTGGAGCAGGAGTAAGTGACATATCTTTAACACATTTTGAAGATTGCATGAGACCGGAAGTCATCCAAGTCAAA

upper sequence: LOC_Os03g13790.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G085427_T02 (Zea mays), 3'ss of exon 10
-------gtacggattttcagtgtagtaaacgaactataatattgtaatacatggggcaataataacaaatactaactgttgttccaactttttgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATCTTTGACTCATTTTGAGAATTGCTTGATACCTGAAGACATCCATGCCAAA
       |  |  |  | ||  ||   ||   |   | ||  |    |  ||          ||||    | |||| ||||||  |||| ||||||   | |||||||||||| ||||||||| |||||||| |||||| ||||||||||||||||| || ||||||||| ||||| ||||||| |||| |||||| | ||||
aattgccgcgcaaaaatgcaa-gtgcgaaggaagtcacaacctaacgagtcacttctagcgcataatgcttgctaattgttgt--caacattttgttgttcagGTATGGTTGGGTTTCCCTTGTTGAGCTTGGAGCAGGAGTAAGTGAAATATCTTTAACCCATTTTGAGGATTGCATGATACCAGAAGTCATCCAAGTCAAA
















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|29644350|gb|CB649357.1|CB649357
EST:     GTGGCTGACGTTTTCCTTTCTGTGAATAGCCCATCTGTTTTTCGATTAAG                         GTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATC
genomic: GTGGCTGACGTTTTCCTTTCTGTGAATAGCCCATCTGTTTTTCGATTAAGgtacggattt ... tgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATC
EST: gi|32948415|gb|BP184987.1|BP184987
EST:     GTGGCTGACGTTTTCCTTTCTGTGAATAGCCCATCTGTTTTTCGATTAAG                         GTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATC
genomic: GTGGCTGACGTTTTCCTTTCTGTGAATAGCCCATCTGTTTTTCGATTAAGgtacggattt ... tgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATC
EST: gi|66923617|gb|CX110465.1|CX110465
EST:     GTGGCTGACGTTTTCCGTTCTGTGAATAGCCCATCTGTTTTTCGATTAAG                         GTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATC
genomic: GTGGCTGACGTTTTCCTTTCTGTGAATAGCCCATCTGTTTTTCGATTAAGgtacggattt ... tgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacatggggcaataataacaaatactaactgttgttccaactttttgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATCTTTGACTCATTTTGAGAATTGCTTGATACCTGAAGACATCCATGCCAAA
                      tactaac  putative branch site (score: 0)
                                        ctttttgtc  putative PPT
          aataataacaaatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggattttcagtgtagtaaacgaactataatattgtaatacatggggcaataataacaaatactaactgttgttccaactttttgtcaataagGTATGGTTGGTTTTCCCTTGCTGAGCTTGAAGCAGGCGTAAGTGAAATATCTTTGACTCATTTTGAGAATTGCTTGATACCTGAAGACATCCATGCCAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA