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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGTAAGCAAGGGCAATTACTTGATGTGAAAGCTGGATTTTTCAGAAACTTCCTCTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacctcaacttcgaaatttccgttcgcttttgtatgctcttactattcggttctaaggcctttgtatttcgagggactttgctacaatgttgtaagatcaacaagaaaaacatcattttctttctttttgtgtgtgtgtttttcccccag

Basic information

species Arabidopsis thaliana
transcript AT3G44890.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G44890.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA11G19820.1 (Glycine max), 5'ss of exon 2
TGGGTAAGCAAGGGCAATTACTTGATGTGAAAGCTGGATTTTTCAGAAACTTCCTCTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacctcaacttcgaaatttccgttcgcttttgtatgctcttactattcggttctaaggcctttgtatttcgagggactttgctacaatgttgtaagatcaacaagaaaaacatcattttctttctttttgtgtgtgtgtttttcccccag
| || |||||||||||| | ||||||||||| ||||| ||||||||||| | |||  | ||||  ||||| || || ||| | |||||||  || ||||||||||  |    || |     || |  ||   ||| | ||     ||| | ||   |   ||    ||| ||  |      | ||||    | || |   |  |                                                    
TAGGAAAGCAAGGGCAACTTCTTGATGTGAAGGCTGGCTTTTTCAGAAATTACCTGCTTCCTATGGGAAAAGCACAACTTGTTACTCCACAGCTTCTCAAgtaatgtat---aattaaaccatctaggt---cttatataacacattaattttgtatataaatatttttttacatttcaatattttggactagtgctcggaatttg--------------------------------------------------
















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|164120885|gb|EL967076.1|EL967076
EST:     TTCCTCTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAA                         GGAATTGAAGATGGAAGACGAA
genomic: TTCCTCTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacc ... tttcccccagGGAATTGAAGATGGAAGACGAA
EST: gi|164186041|gb|ES012177.1|ES012177
EST:     GCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAA                         GGAATTGAAGATGGAAGACGAACGGATTAGAGGCAGAGAAGCAAAGG
genomic: GCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacc ... tttcccccagGGAATTGAAGATGGAAGACGAACGGATT-GAGGCAGAGAAGCAAAGG
EST: gi|164210324|gb|ES091270.1|ES091270
EST:     GCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAA                         GGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGG
genomic: GCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacc ... tttcccccagGGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGG
EST: gi|125140476|gb|EL178719.1|EL178719
EST:     CTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAA                         GGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGGGTGAA
genomic: CTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacc ... tttcccccagGGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGGGTGAA
EST: gi|125110539|gb|EL162451.1|EL162451
EST:     TTCCTCTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAA                         GGAATTGAAGATGGAAGACGAACGGAT
genomic: TTCCTCTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacc ... tttcccccagGGAATTGAAGATGGAAGACGAACGGAT
EST: gi|164213223|gb|ES085174.1|ES085174
EST:     GCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAA                         GGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGG
genomic: GCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacc ... tttcccccagGGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGG
EST: gi|124837220|gb|EH921659.1|EH921659
EST:     CTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAA                         GGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGG
genomic: CTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacc ... tttcccccagGGAATTGAAGATGGAAGACGAACGGATTGAGGCAGAGAAGCAAAGG

Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGTAAGCAAGGGCAATTACTTGATGTGAAAGCTGGATTTTTCAGAAACTTCCTCTTGCCTACTGGAAAGGCTCAGCTTATGACTCCACTTCTGCTCAAgtaattcacctcaacttcgaaatttccgttcgcttttgtatgctcttactattcggttctaaggcctttgtatttcgagggactttgctacaatgttgtaagatcaacaagaaaaacatcattttctttctttttgtgtgtgtgtttttcccccag

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