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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttgggtaaatattatcagtagtttctgagctgttgatcatattaaccgggaaaagtagagatgcttgtgggtaatcaaatcttattttccttgtcagATTGCAAAACATTTATGCAAAAGTTCAAGGAAGTTGCTGAGTCTGAAGAAGAGAAAGAAGAGAGCAAAGATGCCGCTGACACTGCTGGCCTTCTTGAGAA

Basic information

species Arabidopsis thaliana
transcript AT1G07140.1
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|124733709|gb|EH825111.1|EH825111
EST:     ATGAGCTTTTCTGTATCCGATTTGCTTCTATTGAGA                         ATTGCAAAACATTTATGCAAAAGTTCAAGGAAGTTGCTGAGTCTGAAGAAG
genomic: ATGAGCTTTTCTGTATCCGATTTGCTTCTATTGAGAgtgagtatga ... tccttgtcagATTGCAAAACATTTATGCAAAAGTTCAAGGAAGTTGCTGAGTCTGAAGAAG
EST: gi|125242245|gb|EL256330.1|EL256330
EST:     GGTGAACTCAAGGATGAGCTTTTCTGTATCCGATTTGCTTCTATTAGAGA                         ATTGCAAAACATTTATGCAAAAG
genomic: GGTGAACTCAAGGATGAGCTTTTCTGTATCCGATTTGCTTCTATT-GAGAgtgagtatga ... tccttgtcagATTGCAAAACATTTATGCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaccgggaaaagtagagatgcttgtgggtaatcaaatcttattttccttgtcagATTGCAAAACATTTATGCAAAAGTTCAAGGAAGTTGCTGAGTCTGAAGAAGAGAAAGAAGAGAGCAAAGATGCCGCTGACACTGCTGGCCTTCTTGAGAA
 tattaac  putative branch site (score: 1)
                                     tcttattttccttgtc  putative PPT
                             taatcaaatcttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttgggtaaatattatcagtagtttctgagctgttgatcatattaaccgggaaaagtagagatgcttgtgggtaatcaaatcttattttccttgtcagATTGCAAAACATTTATGCAAAAGTTCAAGGAAGTTGCTGAGTCTGAAGAAGAGAAAGAAGAGAGCAAAGATGCCGCTGACACTGCTGGCCTTCTTGAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
attttgg
- - - - - - - - - - - - - - - - - - - - - - - - - -ggaaaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aatcaaa