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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtctctcttcctaattctgcaattgaaatcatcaaatgtatgcataagaaacctaatttgtagaaaaatcatcttgctttatactgatgattggttgattgaatttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGGAACCACGGCTCGTGGGCTTCCTTATGCGGAAGAAGCAATCACCAAAGCT

Basic information

species Arabidopsis thaliana
transcript AT5G43780.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G38760.1 (Glycine max), 3'ss of exon 1
gtaagtctctcttcctaattctgcaattgaaatcatcaaatgtatgcataagaaacctaatttgtagaaaaatcatcttgctttatactgatgattggttgattgaatttgaata-----gTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGGAACCACGGCTCGTGGGCTTCCTTATGCGGAAGAAGCAATCACCAAAGCT
                     || |   |  ||  |  | |   |  |||   | | |  |||   |     |  | || |||| |  ||     |  ||   |   ||||  ||     ||||||||||||| |||||||| ||||||||| |||| ||  |||| ||||||||||  || | ||| || |||||||  ||| || | || ||||| |||
---------------------tgtacgagtgattcttgatttattctatagtcatctttttttactgttttgttttgttcctttcttatggcttatacttttcttcttttggttatttcagTATTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCATTGCCCCTGGCCTACCTTATGTTGAACAAACTATAACCAATGCT

upper sequence: AT5G43780.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G28980.2 (Glycine max), 3'ss of exon 1
gtaagtctctcttcctaattctgcaattgaaatcatcaaatgtatgcataagaaacctaatttgtagaaaaatcatcttgctttatactgatgattggttgattgaatttgaata-----gTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGGAACCACGGCTCGTGGGCTTCCTTATGCGGAAGAAGCAATCACCAAAGCT
                  || |   | |||  |  |  | |   |  |||   |  |   ||| ||      |  |  |  |   | |  |||  |  |   ||   ||||  ||     || |||||||||| |||||||| ||||||||| |||| ||  |||| ||||||||||| || | ||| || || ||||  ||| || | || ||||| |||
-----------------gttgtatgaatga--ttcttgatttattctatagtcattcc--tttttaactgttttcttctcttcctttcctatggcttatacttttcttttggttatttcagTGTTGAGATTTATAAGCATCCTAAAGAAGAAAGAATAGCCCGAACTTGGGGAACCACTGCCCCTGGCCTACCCTATGTTGAACAAACTATAACCAATGCT
















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|146217030|gb|ES431053.1|ES431053
EST:     CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGA                         TATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
genomic: CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGAgtaagtctct ... atttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
EST: gi|116475583|gb|EG518175.1|EG518175
EST:     CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGA                         TATTGAGATTTACAAGCATCCCAAGGAAGAACGAATCGCGAGAACATGGGG
genomic: CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGAgtaagtctct ... atttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
EST: gi|145309240|gb|ES323575.1|ES323575
EST:     CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGA                         TATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
genomic: CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGAgtaagtctct ... atttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
EST: gi|116436094|gb|EG478686.1|EG478686
EST:     CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGA                         TATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
genomic: CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGAgtaagtctct ... atttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
EST: gi|116407563|gb|EG450155.1|EG450155
EST:     CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGA                         TATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
genomic: CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGAgtaagtctct ... atttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
EST: gi|116475594|gb|EG518186.1|EG518186
EST:     CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGA                         TATTGAGATTTACAAGCATCCCAAGGAAGAACGAATCGCGAGAACATGGGG
genomic: CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGAgtaagtctct ... atttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
EST: gi|116436216|gb|EG478808.1|EG478808
EST:     CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGA                         TATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG
genomic: CAAGTCACACTCGTTGACTCGGTTGGTAATCCCATCGCGATTCTCAACGAgtaagtctct ... atttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagaaaaatcatcttgctttatactgatgattggttgattgaatttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGGAACCACGGCTCGTGGGCTTCCTTATGCGGAAGAAGCAATCACCAAAGCT
                                        attgaatttgaata  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtctctcttcctaattctgcaattgaaatcatcaaatgtatgcataagaaacctaatttgtagaaaaatcatcttgctttatactgatgattggttgattgaatttgaatagTATTGAGATTTACAAGCATCCCAAAGAAGAACGAATCGCGAGAACATGGGGAACCACGGCTCGTGGGCTTCCTTATGCGGAAGAAGCAATCACCAAAGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA