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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGATGAGATGGCCAGCTTGCTTAGTTGCCAACGGCCTCCTCAAAAGCTCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgttagtgttggtaggagaagagcataccttcttatgcagtctgagcttttgctaatgacattttgttcctgctgatag

Basic information

species Oryza sativa
transcript LOC_Os06g02130.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02130.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G429113_T01 (Zea mays), 5'ss of exon 1
TCCAGATGAGATGGCCAGCTTGCTTAGTTGCCAACGGCCTCCTCAAAAGCTCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgttagtgttggtaggagaagagcataccttcttatgcagtctgagctttt------gctaatgacattttgttcctgctgatag----------
    || |||||| ||   |||||||| |||||||| ||||||   || ||||||||||||||||||||||| || ||||||||||| ||||||||||||||||  ||     ||| |||  ||||| | |      | | |||||  || ||||| |      ||| || || || |||| ||||||| |           
CGACGAGGAGATGACCGATTTGCTTAGCTGCCAACGACCTCCTGGGAACCTCAAGCCTGGAAGATATTGGTATGATAAGGAGTCAGGATTGTGGGGAAAGgtaattct-----tgtcggtttgagaaaaccgg----tttcatgcaacctcagcttctccagctgctgataacgttatgtttctgctgacatatactcgtag
















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|88580375|gb|CI697297.1|CI697297
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|29622507|gb|CB627518.1|CB627518
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|88584995|gb|CI702594.1|CI702594
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|58664370|gb|CK053056.1|CK053056
EST:     CAAGCCTGGAAGCATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: CAAGCCTGGAAG-ATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|88334602|gb|CI676384.1|CI676384
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|88589414|gb|CI707287.1|CI707287
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|29622064|gb|CB627075.1|CB627075
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|88589015|gb|CI706866.1|CI706866
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|88585156|gb|CI702766.1|CI702766
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
EST: gi|88451771|gb|CI694540.1|CI694540
EST:     TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAG                         GAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA
genomic: TCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgt ... ctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGATGAGATGGCCAGCTTGCTTAGTTGCCAACGGCCTCCTCAAAAGCTCAAGCCTGGAAGATATTGGTACGACAAGGAGTCAGGCTTGTGGGGAAAGgtaagcctgttagtgttggtaggagaagagcataccttcttatgcagtctgagcttttgctaatgacattttgttcctgctgatag

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG