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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtggctgaaccttttgttggtttctactcttcattttccatttctttaaaatggaatctgacaatgtatattttgtgtcctttcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTGATGGCCGAGTTTCCTTCAGCCAAGCCACCACTTGGTGTCTTCTTCGCTG

Basic information

species Arabidopsis thaliana
transcript AT4G30210.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: LOC_Os08g14570.1 (Oryza sativa), 3'ss of exon 10
gtggctgaaccttttgtt--ggtttctactcttcattttccatttctttaaaatggaat--ctgacaatgtatattttgtgtcctttcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTGATGGCCGAGTTTCCTTCAGCCAAGCCACCACTTGGTGTCTTCTTCGCTG
||   |     |||  ||  | | ||| |||    |||     | || |  |||  |||    || ||| |  || |  ||   ||       |||||||| ||| |  | ||||| || | |||||||||||||||| | || |||||||| ||||| |||||||| ||||| ||||| || |||||||| || |
gtcagttcttttttctttcagatatctgctcacgctttcatcatcctatggaatacaataatcgaaaatcttaatatcatgcttttcatgattcagGATGAGTATGCTCAATGGGTTGTTGCGAGTCAAAGAAGTCTATTAGAAGTGATGGCAGAGTTCCCTTCAGCAAAGCCTCCACTAGGAGTCTTCTTTGCAG

upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 11
gtggctgaaccttttgttggtttctactcttcattttccatttctttaaaatggaatctgacaatgtatattttgtgtcctttcaaca--------acagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTGATGGCCGAGTTTCCTTCAGCCAAGCCACCACTTGGTGTCTTCTTCGCTG
                   |||   | | ||||   | ||  ||||| | ||| || |||      | | || ||  ||   | |  |        ||||||||||||| || | |||||||| |  ||||| |||||||| |||||| | ||||| || || || ||||||||||| |||||||| || ||||| || |
-------------------gttgggaattttca---tgcagatctttgatatgaaaactggttccct-tgttatgcctctcatgagaatatgttttacagGATGAATATGCACAATGGGTAGTTGCAAGTCAGAGAAGTCTCCTTGAGATAATGGCTGAATTCCCATCAGCCAAGCCTCCACTTGGAGTTTTCTTTGCAG
















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|116436419|gb|EG479011.1|EG479011
EST:     CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAA-G--                         GATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
genomic: CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGGTTgtggctgaac ... tcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
EST: gi|86044356|gb|DR340111.1|DR340111
EST:     CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGG--                         -ATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
genomic: CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGGTTgtggctgaac ... tcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
EST: gi|86044357|gb|DR340112.1|DR340112
EST:     CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAA-G--                         GATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
genomic: CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGGTTgtggctgaac ... tcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
EST: gi|86044360|gb|DR340115.1|DR340115
EST:     CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAA-G--                         GATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
genomic: CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGGTTgtggctgaac ... tcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
EST: gi|86044358|gb|DR340113.1|DR340113
EST:     CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGG--                         -ATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG
genomic: CTACCGAAGCAGAACGATTAAAACACCTTGCTTCACCTGCTGGAAAGGTTgtggctgaac ... tcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccatttctttaaaatggaatctgacaatgtatattttgtgtcctttcaacaacagGATGAATATTCAAAGTGGGTAGTAGAGAGTCAAAGAAGTCTACTTGAGGTGATGGCCGAGTTTCCTTCAGCCAAGCCACCACTTGGTGTCTTCTTCGCTG
                  atctgac  putative branch site (score: 3)
                                 ttttgtgtcctttc  putative PPT
                       acaatgtatatttt  TA-rich tract