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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAATTTCAGAACATCGATGTCAATCCTCCTAAAGGAACTCGTGATTTCCCTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaattacatgaactctatgttttgtttctgcaattcttcttttggttcgatgaaattttgaatactgtccgtaaagtttgacacttttatctgtttattttgctttgaag

Basic information

species Arabidopsis thaliana
transcript AT5G03406.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03406.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA03G34050.1 (Glycine max), 5'ss of exon 1
AGAATTTCAGAACATCGATGTCAATCCTCCTAAAGGAACTCGTGATTTCCCTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgt---cagagaatt--acatgaact-ctatgttttgtttc-tgca-attcttcttttggttcgatgaaattttgaatactgt-ccgtaaagtttgacacttttatctgtttattttgctttgaag
 ||| |||| || ||||| || |||||||| || || || || || ||||| || ||||| |||||  | ||||||||||||||||| || |||||||||||    |  |  ||  ||   || | ||   ||  ||||| |||  || | |  ||  | ||| | |  || ||  |  | | |  ||   |||||   |||| |  ||| | | ||      ||
TGAAGTTCAAAAGATCGACGTGAATCCTCCCAAGGGGACGCGCGACTTCCCGCCCGAGGACATGCGCTTGCGCAACTGGCTCTTCAATCATTTCAAAGAGgtgtgtatggttttggactcaaattgctcaattccgtttcgtgcctatgcatgcttcagctcggtta--ttgtgttttttatgctttagtctttgatttttttgttcgttaactgtgaggattag

upper sequence: AT5G03406.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv08s0040g01360.t01 (Vitis vinifera), 5'ss of exon 1
AGAATTTCAGAACATCGATGTCAATCCTCCTAAAGGAACTCGTGATTTCCCTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaattacatgaactctat--gttttgtttctgcaattcttcttttggttcgatgaaattttgaatactgtccgtaaagtttgacacttttatctgtttattttgctttgaag
     | ||||| || |||||||||||||| | |||||| || |||||||| || ||||||||||| |||||||||||||| || ||||| |||| |||||| || |          |||   |    | | | | || | || ||   || |||   |    | ||||||||  |  |||  |   || | |     |  |                
TTCGGTACAGAAGATTGATGTCAATCCTCCCAGAGGAACCCGAGATTTCCCGCCCGAGGATATGCGCCTCCGCAACTGGCTTTTTAACCATTTCAGAGAGgttagggtccctatcttacttcgtcgaatatatatatgtattttttaaatttgttttctttg-tcttgaatacc-ttggtagggaaagaaaatggacgcaat----------------
















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|116437285|gb|EG479877.1|EG479877
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437280|gb|EG479872.1|EG479872
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGA
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGA
EST: gi|116437277|gb|EG479869.1|EG479869
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAATCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437263|gb|EG479855.1|EG479855
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437275|gb|EG479867.1|EG479867
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437276|gb|EG479868.1|EG479868
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAATCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437274|gb|EG479866.1|EG479866
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437267|gb|EG479859.1|EG479859
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437268|gb|EG479860.1|EG479860
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437284|gb|EG479876.1|EG479876
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
EST: gi|116437281|gb|EG479873.1|EG479873
EST:     CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAG                         GTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG
genomic: CTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaat ... tgctttgaagGTCTCACGGTTATTTGGGTATGAGGAAGTGGATTTTCCAGTACTGGAGACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAATTTCAGAACATCGATGTCAATCCTCCTAAAGGAACTCGTGATTTCCCTCCTGAGGATATGCGACTCCGCAACTGGCTCTTCAACCACTTCAAAGAGgtcagagaattacatgaactctatgttttgtttctgcaattcttcttttggttcgatgaaattttgaatactgtccgtaaagtttgacacttttatctgtttattttgctttgaag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT