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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctacagagacatgttgcatttaacgtataattttgttttcgcttatgatttgttttcagttttcacttaacaaacaatgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT

Basic information

species Arabidopsis thaliana
transcript AT2G18230.1
intron # 7
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G18230.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA11G07530.1 (Glycine max), 3'ss of exon 7
-------gtatcctacagagacatgttgcatttaacgtat-aattttgttttcgct--tatgatttgttttcag--ttttcacttaacaaacaatgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT
             || | |    | ||  ||  |   ||| |||      | | ||  | | | | |||| | |  | ||  |||| |     |   |   |||||||||||| |||||||| | ||| || |||||||  || || || ||| |||||||||| || || |||||| |||||||
tttggtgaccatttaaataactttcttctatcaatgctatcaatgccacatcccctggtttcagtggtttgctgcatgtttccttagcttgtcacact---agACAAGAAGAATGAGAACAAAATAGTTGATGTTGAAGACTTTCTACCAGCTGAAGCTGCCATTGATGCCATCAAGTACTCCAT
















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|116443156|gb|EG485748.1|EG485748
EST:     AGAGCTTCCCCCTCCCCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACT                         ACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
genomic: AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACTgtatcctaca ... atgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
EST: gi|116443161|gb|EG485753.1|EG485753
EST:     AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACT                         ACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
genomic: AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACTgtatcctaca ... atgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
EST: gi|116451434|gb|EG494026.1|EG494026
EST:     AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACT                         ACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
genomic: AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACTgtatcctaca ... atgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
EST: gi|86075558|gb|DR371315.1|DR371315
EST:     AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACT                         ACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
genomic: AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACTgtatcctaca ... atgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
EST: gi|116451435|gb|EG494027.1|EG494027
EST:     AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACT                         ACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC
genomic: AGAGCTTCCCCCTCACCGTCTAGCTGAAATCCGTCGCTTCTTTGAGGACTgtatcctaca ... atgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgttttcgcttatgatttgttttcagttttcacttaacaaacaatgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT
 tcacttaac  putative branch site 
                                              tgttttt  putative PPT
           ttatgatttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctacagagacatgttgcatttaacgtataattttgttttcgcttatgatttgttttcagttttcacttaacaaacaatgtttttagACAAGAAGAACGAGAACAAGAAAGTCGACGTTGAAGCTTTCCTTCCCGCTCAAGCTGCCATAGACGCTATCAAGGACTCCAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC