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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctgttagtgttggtaggagaagagcataccttcttatgcagtctgagcttttgctaatgacattttgttcctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGAAAGCTTCAGCCCAATGCCAGTAATGGCAACACTCAGGTTTATATGAATG

Basic information

species Oryza sativa
transcript LOC_Os06g02130.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g02130.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G429113_T01 (Zea mays), 3'ss of exon 1
gtaagcctgttagtgttggtaggagaagagcataccttcttatgcagtctgagctttt------gctaatgacattttgttcctgctga----------tagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGAAAGCTTCAGCCCAATGCCAGTAATGGCAACACTCAGGTTTATATGAATG
||||  ||     ||| |||  ||||| | |      | | |||||  || ||||| |      ||| || || || |||| |||||||          |||||||| ||||||||||||||  |  | ||||||||||| | |||||| ||||||||||||||  |||| ||||| |||| | |||||||||  || || |
gtaattct-----tgtcggtttgagaaaaccgg----tttcatgcaacctcagcttctccagctgctgataacgttatgtttctgctgacatatactcgtagGAAGGTGAAAAGCCAGACAGCATCATTAGCACTAACCTCAACTTTAACGGAAAGCTTCAGCCTGATGCTAGTAACGGCACCGCTCAGGTTTTCATTAACG
















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


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ataccttcttatgcagtctgagcttttgctaatgacattttgttcctgctgatagGAAGGAGAAAAGCCAGACAGGGTTGTCAGCACTAACCTAACCTTTAATGGAAAGCTTCAGCCCAATGCCAGTAATGGCAACACTCAGGTTTATATGAATG
                          tgctaat  putative branch site (score: 2)
                                     ttttgttcct  putative PPT
                                    attttgtt  TA-rich tract