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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatgtgttgtgttatgagactctttatgattcatcggtttttatcattgatcttatgatgtgaatccatcgatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGTATTTGCCTTGATATTTTGAAAGAGCAATGGAGCCCTGCTCTTACTATCT

Basic information

species Arabidopsis thaliana
transcript AT3G08690.1
intron # 3
splice site 3'
intron type U2

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|86029019|gb|DR324772.1|DR324772
EST:     TTTTGGTTTCTATTCATTTTCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|86029013|gb|DR324766.1|DR324766
EST:     TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|116447434|gb|EG490026.1|EG490026
EST:     GGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: GGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|86029016|gb|DR324769.1|DR324769
EST:     TTTTGGTTTCTATTCATTTTCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|86029017|gb|DR324770.1|DR324770
EST:     TTTTGGTTTCTATTCATTTTCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|116447417|gb|EG490009.1|EG490009
EST:     TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|86029011|gb|DR324764.1|DR324764
EST:     TTTTGGTTTCTATTCATTTTCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|86077618|gb|DR373375.1|DR373375
EST:     TTTTGGTTTCTATTCATTTTCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|19875312|gb|AU236143.1|AU236143
EST:     TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|86029015|gb|DR324768.1|DR324768
EST:     TTTTGGTTTCTATTCATTTTCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|19741608|gb|AU226961.1|AU226961
EST:     ATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: ATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|86029014|gb|DR324767.1|DR324767
EST:     TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
EST: gi|301502421|gb|HO207961.1|HO207961
EST:     TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAG                         GTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT
genomic: TTTTGGTTTCTATTCATTTCCCTCCGGATTATCCTTTCAAGCCACCAAAGgtaatgtgtt ... gatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgattcatcggtttttatcattgatcttatgatgtgaatccatcgatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGTATTTGCCTTGATATTTTGAAAGAGCAATGGAGCCCTGCTCTTACTATCT
                   cattgat  putative branch site (score: 4)
            tttttatcattgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatgtgttgtgttatgagactctttatgattcatcggtttttatcattgatcttatgatgtgaatccatcgatcttgcagGTGTCTTTTAAGACTAAGGTGTACCATCCAAACATCAATAGCAATGGAAGTATTTGCCTTGATATTTTGAAAGAGCAATGGAGCCCTGCTCTTACTATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA