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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctcttttggttttgatctcttgtatatccttaagtaatagttgtgatgatcttagagtagattattctggctgttgattgaaacatatatttacttctctatcttccataatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCACCAAAGTTATACCACATGAAGATTGCATTGGGACATTACAAGAACTGGT

Basic information

species Arabidopsis thaliana
transcript AT5G16710.1
intron # 4
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|19799493|gb|AU230783.1|AU230783
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAA-GACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|164180173|gb|ES070023.1|ES070023
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGA
EST: gi|116480640|gb|EG523232.1|EG523232
EST:     AAGTTTTGTTGGACGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|86076765|gb|DR372522.1|DR372522
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480635|gb|EG523227.1|EG523227
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480632|gb|EG523224.1|EG523224
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCGCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480636|gb|EG523228.1|EG523228
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480645|gb|EG523237.1|EG523237
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480622|gb|EG523214.1|EG523214
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480638|gb|EG523230.1|EG523230
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|124784041|gb|EH873813.1|EH873813
EST:     TTTTGTTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: TTTTG-TTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480643|gb|EG523235.1|EG523235
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA
EST: gi|116480631|gb|EG523223.1|EG523223
EST:     AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAAT                         GGCCCTTTCATAAATGGAGAGAAGATCGCGGCAGCAGATTTGTCCTTGGCA
genomic: AAGTTTTGTTGGATGAGCTTACTACATTCAACGATTATATCAAGGACAATgtaagctctt ... taatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attctggctgttgattgaaacatatatttacttctctatcttccataatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCACCAAAGTTATACCACATGAAGATTGCATTGGGACATTACAAGAACTGGT
        tgttgat  putative branch site (score: 4)
                              cttctctatcttccat  putative PPT
             attgaaacatatattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctcttttggttttgatctcttgtatatccttaagtaatagttgtgatgatcttagagtagattattctggctgttgattgaaacatatatttacttctctatcttccataatgtgaagGGCCCTTTCATAAATGGAGAGAAGATCTCGGCAGCAGATTTGTCCTTGGCACCAAAGTTATACCACATGAAGATTGCATTGGGACATTACAAGAACTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC