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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttttcattacccccaattcatattttgttcttaagtgttttgattaatctgtttccccattatcctcttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGGAAAGAACTAGTTCTCGGGATCATCGACTTCATGAGACAGTACACATGGG

Basic information

species Arabidopsis thaliana
transcript AT1G71010.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G71010.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G34030.1 (Glycine max), 3'ss of exon 12
----------gtaagtgttttcattacccccaattcatattttgtt--cttaagtgttttgattaatctgtttccccattatcctcttgtggtt----agTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGGAAAGAACTAGTTCTCGGGATCATCGACTTCATGAGACAGTACACATGGG
           | |        | ||     || |   | ||| ||   || ||| | | | |    ||   |   | || |||  ||||||||    ||||||| || || |||||||| || |||||||||||| ||||||| ||||| || ||||| ||||| |||||||| || ||||||||||| ||||||||||
atggttttactttatgacccaaaatatttttaactagcagtttcttggttttagtatatggttgttactcactttactttctccctttgtggttcttcagTCTGTTGACGTTATGGACTATTCTTTGCTGGTTGGAGTCGACGATGAGCGCAAGGAACTGGTTCTGGGGATCATTGATTTCATGAGACAATACACATGGG

upper sequence: AT1G71010.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA20G01680.1 (Glycine max), 3'ss of exon 17
--------gtaagtgttttcattacccccaattcatattttgttctta-------agtgtt-ttgattaatctgtttccccattatcctcttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGGAAAGAACTAGTTCTCGGGATCATCGACTTCATGAGACAGTACACATGGG
         |  || ||  || |  |   | |  |    |||    ||         ||||  |  ||| |   ||||  ||  ||  |    |  | |||||||  |||| |||||||| || |||||||||||  | ||||| ||  | |||||||| ||| | |||||||| || ||||||||||| ||||||||||
agccatttcttggtcttaccacttacttaagtgtagcaattgcctctattgcaaggttgttacttgttacttactttctacaacatttttggttcttcagTCTGTTTATGTGATGGACTATTCTTTGCTGGTTGGGGTGGACGATGATAGCAAAGAACTGGTTTTGGGGATCATTGATTTCATGAGACAATACACATGGG
















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|116481199|gb|EG523791.1|EG523791
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
EST: gi|116444965|gb|EG487557.1|EG487557
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
EST: gi|116448284|gb|EG490876.1|EG490876
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTTTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
EST: gi|116377741|gb|EG420333.1|EG420333
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCT                         TCTGTGGATGAAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
EST: gi|124786988|gb|EH876667.1|EH876667
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTC
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTC
EST: gi|86085487|gb|DR381246.1|DR381246
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAACTTCTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
EST: gi|124961371|gb|EL035904.1|EL035904
EST:     CGACACCAATTTCTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
EST: gi|116416458|gb|EG459050.1|EG459050
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACCCCAATTTCTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
EST: gi|116412488|gb|EG455080.1|EG455080
EST:     CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCT                         TCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG
genomic: CCAAGAGAAGCTTGGAAAGAGCGATATGGAACGACACCAATTTCTTGGCTgtaagtgttt ... ttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttcttaagtgttttgattaatctgtttccccattatcctcttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGGAAAGAACTAGTTCTCGGGATCATCGACTTCATGAGACAGTACACATGGG
                   gattaat  putative branch site (score: 3)
                         tctgtttccccattat  CT-rich tract
               ttttgattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttttcattacccccaattcatattttgttcttaagtgttttgattaatctgtttccccattatcctcttgtggttagTCTGTGGATGTAATGGACTACTCATTGCTGGTTGGATTCGACGAAGAGCGGAAAGAACTAGTTCTCGGGATCATCGACTTCATGAGACAGTACACATGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC