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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtattccccccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCCGAGGTGCCCTCCGAGGACGTCGTCG

Basic information

species Oryza sativa
transcript LOC_Os01g62420.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 1
gtaagtattccccccagcactagtcgtctcacaatccagattccggatgagccggagacgctgctgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCCGAGGTGCCCTCCGAGGACGTCGTCG
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gtaagt---ccccctaggacccag-gctccaggcaccaccgttctctcgatttgaattcgacgttacgcagagttttggtttgatctct---gatggcatccgct-cccccgtgtgcagAACGGTACTGGCGAGGACGTGAAGAAGATCGTCACCGTGCTCAACCAAGCCGAGGTGCCCTCTGAAGACGTCGTCG
















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|33692885|gb|CF321124.1|CF321124
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|88575287|gb|CI669432.1|CI669432
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|2312292|gb|C28447.1|C28447
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|25800835|gb|CA756796.1|CA756796
EST:     GGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: GGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|88391559|gb|CI600748.1|CI600748
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|88722774|gb|CI746284.1|CI746284
EST:     ATCCATCCATGGCTGCCAGGAAGTCCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|86830034|gb|CI288672.1|CI288672
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|427784|gb|D23922.1|D23922
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCC
EST: gi|33686817|gb|CF315056.1|CF315056
EST:     ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGC                         AATGGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGC
genomic: ATCCATCCATGGCTGCCAGGAAGTTCTTCGTCGGCGGCAACTGGAAATGCgtaagtattc ... ctgcgtgcagAAT-GGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgagtgatgaggcttgggttttatcgatgcgctgcgctgttgctgcgtgcagAATGGGACAGGGGAGGACGTGAAGAAGATCGTCACCGTCCTCAACGAGGCCGAGGTGCCCTCCGAGGACGTCGTCG
 tgctgat  putative branch site (score: 3)
                     ttttat  TA-rich tract