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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcattccttcttctttttttcggtcttatgatgcacttgtttttgtgcaattgaccttctagtgttctttgttgaaaaagggttcatttgacaacttgcatacttccagctaagaatttgcgtgtggacgtttaattctttaatttatgtctgtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTCAGGAGATGGAACTGAGCAAGTTTTGTTGGATGAGCTTACTACATTCAAC

Basic information

species Arabidopsis thaliana
transcript AT5G16710.1
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|19878642|gb|AU239473.1|AU239473
EST:     GAGAAGTATNCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAANATCTTTTCCACATTTGTCGG
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGG
EST: gi|116480640|gb|EG523232.1|EG523232
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|86076765|gb|DR372522.1|DR372522
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|116480635|gb|EG523227.1|EG523227
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|116480632|gb|EG523224.1|EG523224
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|116480636|gb|EG523228.1|EG523228
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCCGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|124857942|gb|EH942379.1|EH942379
EST:     GAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|116480645|gb|EG523237.1|EG523237
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|116480622|gb|EG523214.1|EG523214
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|116480638|gb|EG523230.1|EG523230
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|47829198|gb|CK118882.1|CK118882
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|124732208|gb|EH823610.1|EH823610
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGA
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGA
EST: gi|125028537|gb|EL100806.1|EL100806
EST:     GAAGTATCCTGAGCCTCCTCTTGTCTTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATT
genomic: GAAGTATCCTGAGCCTCCTCTTG-C-TACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATT
EST: gi|125103509|gb|EL157891.1|EL157891
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGAT
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGAT
EST: gi|116480643|gb|EG523235.1|EG523235
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGGTCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|116480631|gb|EG523223.1|EG523223
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTC
EST: gi|125295452|gb|EL309537.1|EL309537
EST:     GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGT                         TGGATCGAAGATCTTTTCCACATTTGTCGGTTTT
genomic: GAGAAGTATCCTGAGCCTCCTCTTGCTACCCCACCTGAAAAGGCTTCAGTgtaagcattc ... gtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agctaagaatttgcgtgtggacgtttaattctttaatttatgtctgtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTCAGGAGATGGAACTGAGCAAGTTTTGTTGGATGAGCTTACTACATTCAAC
                              ctttaat  putative branch site (score: 4)
                                          tctgtttct  putative PPT
                       tttaattctttaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcattccttcttctttttttcggtcttatgatgcacttgtttttgtgcaattgaccttctagtgttctttgttgaaaaagggttcatttgacaacttgcatacttccagctaagaatttgcgtgtggacgtttaattctttaatttatgtctgtttctgcagTGGATCGAAGATCTTTTCCACATTTGTCGGTTTTCTGAAGAGCAAAGATTCAGGAGATGGAACTGAGCAAGTTTTGTTGGATGAGCTTACTACATTCAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT