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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCTAAGGTTCAATTCAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgtactcttgtttacgagattctttgtttctgaacgaaatgatatcttggccatttgagaacaaatgattactttacatctctggttggttga...

Basic information

species Arabidopsis thaliana
transcript AT2G19730.3
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G19730.3 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os01g51020.1 (Oryza sativa), 5'ss of exon 2
AACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCTAAGGTTCAATTCAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgtactcttgtttacgagattctttgtttctgaacgaaatgatatcttggccatttgagaac-aaatgattactttacatctctggttggttga-
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AATTCATTCCTGGTCAAGCAGTTCGGCAATGGCAATGCCAAGGTTCAGTTCAGCAAGGAGCCCAACAACCTGTACAATGTCCACTCTTACAAGCATTCTGgtaa-ttaatggt-tggttggcatgcttctcttgatatgcatgtc-tcccgtggcactctcttgagtcttgactggttgtgctgttcatttggtcttttcag
















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|124943508|gb|EL019684.1|EL019684
EST:     CACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|164042713|gb|ES002199.1|ES002199
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAA-CAAAAAGACTGTGACCATCCAGGCCGCTG-CAAGGACC
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACC
EST: gi|164181652|gb|ES036916.1|ES036916
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTTCTTGCAAACAAAA
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGT-CTTGCAAACAAAA
EST: gi|125097291|gb|EL153799.1|EL153799
EST:     CAGCAAGGAGACTAACAACTTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCG
EST: gi|86066023|gb|DR361780.1|DR361780
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|86066020|gb|DR361777.1|DR361777
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|164158810|gb|ES085549.1|ES085549
EST:     GACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAA
genomic: GACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAA-GACTGTGACCATCCAGGCCGCTGACAAGGACCAA
EST: gi|86066015|gb|DR361772.1|DR361772
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|164137302|gb|ES125399.1|ES125399
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAA
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAA
EST: gi|86066017|gb|DR361774.1|DR361774
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|86066001|gb|DR361758.1|DR361758
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAWGACTGTGACCATCCAGGCCGCTGACAAGGACCAA
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAA-GACTGTGACCATCCAGGCCGCTGACAAGGACCAA
EST: gi|86079143|gb|DR374900.1|DR374900
EST:     CAACCTCACCAACGTTCACTCTTMCAAGCACTCTG                         GTCTTGCAAACAWAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|164010394|gb|ES056080.1|ES056080
EST:     AGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTAG                         GTCTTGCAAACAAAA-GACTGTGACCATC
genomic: AGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCT-Ggtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATC
EST: gi|86066019|gb|DR361776.1|DR361776
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|164179018|gb|ES042089.1|ES042089
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAA
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAA
EST: gi|164114901|gb|ES209376.1|ES209376
EST:     CAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|116452423|gb|EG495015.1|EG495015
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|86066018|gb|DR361775.1|DR361775
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|47830640|gb|CK120324.1|CK120324
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|86066025|gb|DR361782.1|DR361782
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
EST: gi|86066021|gb|DR361778.1|DR361778
EST:     CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTG                         GTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG
genomic: CAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgt ... gtggtttcagGTCTTGCAAACAAAAAGACTGTGACCATCCAGGCCGCTGACAAGGACCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACTGTTTCTTGGTGAAGCAGTTCGGTAGAGGAAACTCTAAGGTTCAATTCAGCAAGGAGACTAACAACCTCACCAACGTTCACTCTTACAAGCACTCTGgtaaatttgtactcttgtttacgagattctttgtttctgaacgaaatgatatcttggccatttgagaacaaatgattactttacatctctggttggttga

- - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacgaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaacaaa