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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttttgttttgttttgtagagtattattattgatttgagtagagtagtgtgaggtttggtttgtgatgatgtttaatagagtactctctggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTGCATAGCTTGTACCAAAGCAGACGGAGGTGAAGAAGTCGAACATGGAGCG

Basic information

species Arabidopsis thaliana
transcript AT1G31880.1
intron # 2
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|116385358|gb|EG427950.1|EG427950
EST:     AATAATCTCAGAATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTC
genomic: AATAATCTCAG-ATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTT-
EST: gi|116385343|gb|EG427935.1|EG427935
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385353|gb|EG427945.1|EG427945
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTC-AAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385350|gb|EG427942.1|EG427942
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385347|gb|EG427939.1|EG427939
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385355|gb|EG427947.1|EG427947
EST:     CAATAATCCCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385354|gb|EG427946.1|EG427946
EST:     CAATAATCCCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385341|gb|EG427933.1|EG427933
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385348|gb|EG427940.1|EG427940
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385352|gb|EG427944.1|EG427944
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTC-AAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385342|gb|EG427934.1|EG427934
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
EST: gi|116385359|gb|EG427951.1|EG427951
EST:     CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAG                         GTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG
genomic: CAATAATCTCAGATCATATCGCTTCATTTCTCAGATATCGAAACACAAAGgtgagtgagt ... ggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtgtgaggtttggtttgtgatgatgtttaatagagtactctctggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTGCATAGCTTGTACCAAAGCAGACGGAGGTGAAGAAGTCGAACATGGAGCG
                          gtttaat  putative branch site (score: 4)
                                       ctctctg  putative PPT
                        atgtttaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttttgttttgttttgtagagtattattattgatttgagtagagtagtgtgaggtttggtttgtgatgatgtttaatagagtactctctggttttatagGTCTGAAAAGGCAGAGAACAACTCAAAAAAGAGACCAAAAATGTTTTCTTGCATAGCTTGTACCAAAGCAGACGGAGGTGAAGAAGTCGAACATGGAGCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - -tgttttg
- - - - - - - - - - - - - - - - gatttga
- - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgg