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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAACCAAGGAGCCTGGTATAACATTTGTTGTAGCTAAATTTGATGGTATCCTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcctgcacattcttctcttgtttggactgagttactacattcctgtagtgttaatgctaatatgtcttgttttttacag

Basic information

species Arabidopsis thaliana
transcript AT1G11910.1
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA17G01500.1 (Glycine max), 5'ss of exon 5
CAACCAAGGAGCCTGGTATAACATTTGTTGTAGCTAAATTTGATGGTATCCTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcc----tgcacattct--tctcttgtttggactgag--ttactacattcct---gtagtgttaatgctaatatgtcttgttttttacag-------
|||| | |||||||||| | |||||| | |  || || ||||||||||| || || |||||||| |||||||| || |||||||| |||||||| || |||||||      |  | |||    |  ||  ||| |   ||   ||| |  |||  |    |  ||||| |||| |  |   |       ||| |       
CAACTAGGGAGCCTGGTGTTACATTTTTGGCGGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATGCTGCTCCAGTGTGgtatgttactatttaaatttcgattcctcattttgttagaagtttattgaatttattgaattttgttagtgcttac-tacatcagaccctactggatctaa

upper sequence: AT1G11910.1 (Arabidopsis thaliana), 5'ss of exon 5
lower sequence: GLYMA07G39240.2 (Glycine max), 5'ss of exon 5
CAACCAAGGAGCCTGGTATAACATTTGTTGTAGCTAAATTTGATGGTATCCTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtat--------gcctgcacattcttctcttgtttggactgag--ttactacattcctgtagt---------gttaatgctaa-tatgtcttgttttttacag
|||| | |||||||||| | |||||| | | ||| || ||||||||||| || || |||||||| |||||||| || |||||||| |||| ||| || ||||||           |  |  ||  |  || |||| |   ||   ||| |  |||  |  | |         |  ||||| |  || ||| || || ||    
CAACTAGGGAGCCTGGTGTTACATTTTTGGCAGCCAAGTTTGATGGTATACTGGGACTTGGATTTCAAGAGATATCAGTTGGAAATGCTGTTCCAGTGTGgtatttgttacaatttaaattttgattcctcgttttgttagaagtttattgtatttattgaatcagcctgttgcaaatgcaaggtaagtcctgcttattg---
















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|124916723|gb|EH990597.1|EH990597
EST:     CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTG                         GTACAACATGCTCAAG
genomic: CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcctgc ... ttttttacagGTACAACATGCTCAAG
EST: gi|152033756|gb|BP560644.3|BP560644
EST:     CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTG                         GTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCCGGTTTTTTCATTTTG
genomic: CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcctgc ... ttttttacagGTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCCGGTTTTTTCATTTTG
EST: gi|116417009|gb|EG459601.1|EG459601
EST:     CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTG                         GTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCCGGTTTTTTCATTTTG
genomic: CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcctgc ... ttttttacagGTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCCGGTTTTTTCATTTTG
EST: gi|164021468|gb|ES158328.1|ES158328
EST:     CTTAGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTG                         GTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCC
genomic: CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcctgc ... ttttttacagGTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCC
EST: gi|125238991|gb|EL253076.1|EL253076
EST:     CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTG                         GTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCCGGTTTTTTCATTTTG
genomic: CTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcctgc ... ttttttacagGTACAACATGCTCAAGCAAGGCCTTATCAAGGAGCCGGTTTTTTCATTTTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAACCAAGGAGCCTGGTATAACATTTGTTGTAGCTAAATTTGATGGTATCCTTGGTCTTGGATTCCAAGAGATCTCTGTTGGAAAAGCTGCTCCTGTTTGgtatgcctgcacattcttctcttgtttggactgagttactacattcctgtagtgttaatgctaatatgtcttgttttttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT