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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtctcttatcttgtttggcatagttcagttattttgtgagtgcatttgattaatagtgtacgtttgtttatttatgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGTGCTCATGATGGTTTAGTTGCAGCGCTAGCAGCATCGAGCGCAACAGGCA

Basic information

species Oryza sativa
transcript LOC_Os01g42260.2
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g42260.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 17
gcaagtct-cttatcttgtttg--gcatagttcagttattttg--------tgagtgcatttgattaatagtgtacgtttg--------tttat-ttatgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGTGCTCATGATGGTTTAGTTGCAGCGCTAGCAGCATCGAGCGCAACAGGCA
| |||| | | ||  || ||||   | ||||| | | |||  |        | |  |   ||  | |     ||   |||         ||||| || |||  ||||||| |||||||| |||||||| |||||||||||| |||||||  || ||| ||| ||||| ||||| |||||||| || |||||||| || |||||||| |
gtaagttttcctagtttttttgtaacctagtt-aataattccggagcataatcatagtcctttttcagggaggtggatttaacttctattttatgttttgttatgcagTCCTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAATGCGCATGACGGTTTGGTTGCAGCCCTGGCAGCATCCAGTGCAACAGGGA

upper sequence: LOC_Os01g42260.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G425377_T01 (Zea mays), 3'ss of exon 9
----gcaagtctcttatcttgtttg-gcatagttcagtta-ttttgtgagtgcatttgattaata---gtgtacgtttgtttat---ttatgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGTGCTCATGATGGTTTAGTTGCAGCGCTAGCAGCATCGAGCGCAACAGGCA
    |||| ||  |  ||     || ||||     | |||  |||   |       | | | | |    | ||  |||  || |   | ||||  |||||||||||||||| |||||||| |||||||||||| |||||||  || ||| ||| ||||| ||||| |||||||| || ||| |||| || || ||||| |
ggaggcaattccttggtcaacaatgcgcatgacggatttaactttaccatcagtcctcagtgagatggatttaactttacttctatttcatgttatgcagTCTTTGGAACTTTGGGACATAAGGGAGAAGAACACCATGACCTTCAACAATGCGCATGACGGTTTGGTTGCAGCCCTGGCATCATCCAGTGCTACAGGGA
















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|88221810|gb|CI221766.1|CI221766
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|16576984|gb|BI804280.1|BI804280
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|29681692|gb|CB677967.1|CB677967
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCCCAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86430973|gb|CI083396.1|CI083396
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86431296|gb|CI083719.1|CI083719
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|33690022|gb|CF318261.1|CF318261
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86260005|gb|CI065878.1|CI065878
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|33690021|gb|CF318260.1|CF318260
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACA
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACA
EST: gi|88842163|gb|CI081419.1|CI081419
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|3107062|gb|D42797.1|D42797
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|8404601|gb|AU091955.1|AU091955
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTNGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACNGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|16575961|gb|BI803257.1|BI803257
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|29673281|gb|CB669556.1|CB669556
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|29638960|gb|CB643969.1|CB643969
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|86601890|gb|CI258566.1|CI258566
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGT
EST: gi|38478243|gb|CF962376.1|CF962376
EST:     GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAG                         TCTTTGGAACTCTGGGACATTAGGGAGAAG
genomic: GCGTTTTTCACCCCTCTTACCCATATTTGCTAGTAATTGGATGCTACGAGgcaagtctct ... tgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttgtgagtgcatttgattaatagtgtacgtttgtttatttatgtcgtgcagTCTTTGGAACTCTGGGACATTAGGGAGAAGAACGCCATGACGGTCCACAGTGCTCATGATGGTTTAGTTGCAGCGCTAGCAGCATCGAGCGCAACAGGCA
                  gattaat  putative branch site (score: 3)
                                 tttgtttatttatgt  TA-rich tract