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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatacaagtcaaattatataacatgttgtttgcatttatcttgtttgtcttacttaatttgtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAGAGATGAAGATCCACTGATCGATAGTGATGATGAAAGACCTGAGAGCTTT

Basic information

species Oryza sativa
transcript LOC_Os12g01140.4
intron # 1
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|29624477|gb|CB629488.1|CB629488
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29630119|gb|CB635128.1|CB635128
EST:     CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29681859|gb|CB678134.1|CB678134
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29624448|gb|CB629459.1|CB629459
EST:     CCTGATCAAGTGAATAGAACTAGAGAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29641853|gb|CB646860.1|CB646860
EST:     CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29628293|gb|CB633304.1|CB633304
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29678744|gb|CB675019.1|CB675019
EST:     CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29627346|gb|CB632357.1|CB632357
EST:     CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29630466|gb|CB635475.1|CB635475
EST:     CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29624450|gb|CB629461.1|CB629461
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|58593934|gb|CF992242.1|CF992242
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|58592396|gb|CF990704.1|CF990704
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|66924760|gb|CX111608.1|CX111608
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
EST: gi|29646710|gb|CB651717.1|CB651717
EST:     CCTGATCAAGTGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGG                         TTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG
genomic: CCTGATCAAGGGAATAGAACTAGAAAATCTGGTCTGCGTGCATTTATGGGgtatgcatac ... gtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atataacatgttgtttgcatttatcttgtttgtcttacttaatttgtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAGAGATGAAGATCCACTGATCGATAGTGATGATGAAAGACCTGAGAGCTTT
                                  ttacttaatttgta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcatacaagtcaaattatataacatgttgtttgcatttatcttgtttgtcttacttaatttgtacatgcagTTTTCTTGGTATGGGCCATGGAAGTGTAGAGAAGAACATGCTGAAACCTAGAGATGAAGATCCACTGATCGATAGTGATGATGAAAGACCTGAGAGCTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT