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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGAGATCATGTATGATATGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatcgaatcgtgcactgtccatggaagaaactccaaagaatttttgttttcctcttgaaatactgtaatactaatttcacatatgtcacaatctgttccag

Basic information

species Arabidopsis thaliana
transcript AT2G20360.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20360.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: Vv07s0005g04440.t01 (Vitis vinifera), 5'ss of exon 10
GCAGAGATCATGTATGATATGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatcgaatcgtgcactgtccatggaagaaactccaaagaatttttgttttcctcttgaaatactg--taatactaatttcacatatgtcacaatctgttccag
||||   | |||||||| | ||| |||||||||||||| ||||||||  | || || |||||||| ||||||||| |   |  |      ||||| |         |||       |||||  |     | |   |  ||  |     | |||  ||| |||     ||||       
GCAGCAGTAATGTATGACACGATCCGTGAATGGCCTCGTTATGTGAAAGTGCCTTTCCCAATTGCAAAGgtaaaacaaatatgctgctgttgtccttttttccccttccctttt-cttttgggtgttggtcgggttggtgattggaggtcattggaca-atgggtttatct-------
















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|116401381|gb|EG443973.1|EG443973
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116401379|gb|EG443971.1|EG443971
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116401374|gb|EG443966.1|EG443966
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116401371|gb|EG443963.1|EG443963
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116401378|gb|EG443970.1|EG443970
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116401372|gb|EG443964.1|EG443964
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116401376|gb|EG443968.1|EG443968
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116383740|gb|EG426332.1|EG426332
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116383739|gb|EG426331.1|EG426331
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116387790|gb|EG430382.1|EG430382
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|116401380|gb|EG443972.1|EG443972
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAGTCCCGTTCCCCTTA
EST: gi|164117649|gb|ES004810.1|ES004810
EST:     TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAG                         GCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAG
genomic: TGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatc ... tctgttccagGCAATGGCGGCTCCTCGAGACTTCATGGTGAACAAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGAGATCATGTATGATATGATTCGTGAATGGCCTCGGTATGTGAAGCTTCCGTTTCCAATTGCCAAGgtaaaagatcgaatcgtgcactgtccatggaagaaactccaaagaatttttgttttcctcttgaaatactgtaatactaatttcacatatgtcacaatctgttccag

- - - - - - - - - - - - - - - - - - - - -  TGAAGC