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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcaattgccttccttgtctttcttttcaaggaaaaaagggaaacaacactggcttcattttaattttattgcaaacaatccctgaaacttgttctaaacaaacattagtccttttcctcatagaccactttcatatttctgtacaatgcatttttttcatagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG

Basic information

species Oryza sativa
transcript LOC_Os01g67220.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g67220.3 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G044092_T01 (Zea mays), 3'ss of exon 3
gtagcaattgccttccttgtctttcttttcaaggaaaaaagggaaacaacactggcttcattttaattttattgcaaacaatccctgaaacttgttctaaacaaacattagtccttttcctcatagaccactttcatatttctgtacaatgcatttttttcatagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG
                                                      |  |  | | |   ||  | || |  |     ||||     ||  |||||| |  ||  |      |    |  ||| |||   ||  ||   |  |  |   | |||  ||   | ||     ||| ||  || |  |||| |||||||||||||| |||||||| ||| | |||||  | || || |||||||||||||||||| | || ||||||||||
------------------------------------------------------gtattgtct-accattcctacagatga-----gaaaaagaatc--aacaaaaaa-agagcggcgggtggaggggcacattc---ttcttggtaatagggtaactatcaacgaattgaaa-----tgtttgctataaactttt-cagGAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCGCGTATATTTCCTG

upper sequence: LOC_Os01g67220.3 (Oryza sativa), 3'ss of exon 3
lower sequence: AC155376.2_FGT005 (Zea mays), 3'ss of exon 3
gtagcaattgccttccttgtctttcttttcaaggaaaaaagggaaacaacactggcttcattttaattttattgcaaacaatccctgaaacttgttctaaacaaacattagtccttttcctcatagaccactttcatatttctgtacaatgcatttttttc----atagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG
                ||||||  | || | |  ||| ||  | ||| | |        |     |        | | |  | | | | |     | | ||  |||     |  || ||       || |  || || |   |||||| |||||| |||      | | |  |  || ||||||| ||  ||    ||||||||||||||||||| |||||||| ||| | |||||  | || || |||||||||||||||||| |||| ||||||||||
-------------gtattgtctagcattcctataaaagaaaaggaaccataaaaaaaagagggggaggggggctccatc--ttcttaacaacgaatgtgaa--aactgccatttttctctgttcctacaatgttaatttggttgtacattgcattgtttctcaggaaaaaaaaacaatttcttgtttgaaata---tttttcagGAAGACATTGAGCTCATGGCAAGTCTAGGTTTTAGCGCATACAGATTTTCTATATCTTGGGCACGTATATTTCCTG
















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|88575864|gb|CI670009.1|CI670009
EST:     AGATGGGAGCAGTGGAGAAGTTGCACGTTGATCATTACCATCGATACAAG                         GAAGACATTGAACTCATGGCCAGTTTGGGTTCCCGTGCTTATAGATCTTCT
genomic: AGATGGGAGCAGTGGAGAAGTTGCA-GTTGATCATTACCATCGATACAAGgtagcaattg ... gttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
EST: gi|88356318|gb|CI652755.1|CI652755
EST:     TAGATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAG                         GAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
genomic: TAGATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAGgtagcaattg ... gttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
EST: gi|88761211|gb|CI770767.1|CI770767
EST:     TACATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAG                         GAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT
genomic: TAGATGGGAGCAGTGGAGAAGTTGCAGTTGATCATTACCATCGATACAAGgtagcaattg ... gttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acaatgcatttttttcatagagcagtaacttcttgtctgtgatgagttttttcagGAAGACATTGAACTCATGGCCAGTTTGGGTTTCCGTGCTTATAGATTTTCTATATCTTGGCCACGCATATTTCCTG
                      cagtaac  putative branch site (score: 2)
                                              ttttttc  putative PPT
       atttttttcataga  TA-rich tract