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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtattgtctgagaagctgaatagagattgttttatgttttatggtttcactaatttgttctgaaatgtgaattctcagTTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGAGCGGAGGATATAATGATGCTTAACAATGGCTGTCTGTGTTGTACTGTTA

Basic information

species Arabidopsis thaliana
transcript AT1G15730.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G15730.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G180418_T03 (Zea mays), 3'ss of exon 7
--------------------gtattgtctgagaa-gctgaatagagattgttttatgttttatggtttcactaatttgttctgaaatg--tgaattctcagTTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGAGCGGAGGATATAATGATGCTTAACAATGGCTGTCTGTGTTGTACTGTTA
                      ||    |  ||  ||  ||   | || |      |         ||  ||| ||| | |||  ||   | |  |  |||||||| ||||| ||||||||||| ||||| || || || ||||| || ||||| ||||| ||||||||||| || || ||||| || ||||| |||||  
ttactcagttcatgatcaatccatcacttaggagtgcccaactaatat-gcaaggcgaagctgaacttgtctactttttgctgtcattgttcacattgcagTTTGGAGAAGTAGACATTGATGGCTCACTAGTCGCTGCACAAACCGCTGGAGCTGAGGACATAATGATGCTAAATAACGGCTGCCTTTGTTGCACTGTGC
















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|116433950|gb|EG476542.1|EG476542
EST:     ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAG                         TTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGA
genomic: ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAGgtattgtctg ... gaattctcagTTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGA
EST: gi|125310615|gb|EL324700.1|EL324700
EST:     ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAG                         TTTGGTGAAGTCGACATTGATGGA
genomic: ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAGgtattgtctg ... gaattctcagTTTGGTGAAGTCGACATTGATGGA
EST: gi|116474224|gb|EG516816.1|EG516816
EST:     ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAG                         TTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGA
genomic: ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAGgtattgtctg ... gaattctcagTTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGA
EST: gi|116474225|gb|EG516817.1|EG516817
EST:     ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAG                         TTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGA
genomic: ATATATTGACGGGAGATCATGGGAAGCGCATAGCCGTGATTGAGAACGAGgtattgtctg ... gaattctcagTTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattgttttatgttttatggtttcactaatttgttctgaaatgtgaattctcagTTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGAGCGGAGGATATAATGATGCTTAACAATGGCTGTCTGTGTTGTACTGTTA
                        cactaat  putative branch site (score: 2)
                                                ttctc  putative PPT
      ttttatgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtattgtctgagaagctgaatagagattgttttatgttttatggtttcactaatttgttctgaaatgtgaattctcagTTTGGTGAAGTCGACATTGATGGATCACTTGTGGCAGCTCAAACTGCGGGAGCGGAGGATATAATGATGCTTAACAATGGCTGTCTGTGTTGTACTGTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT