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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttctctgtgattaacaatctgttcaatttctcaaaggtgtcttttttatttgattagtatagcttatttttggtttgtttatggcatgctatgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGATCAAGAGGCAAGAGGAATGGGCATTGGCCAAGAAAGATGAAGCTGTAGC

Basic information

species Arabidopsis thaliana
transcript AT2G44120.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44120.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA07G02270.1 (Glycine max), 3'ss of exon 1
-------ttctctgtgattaacaatctgttcaatttctcaaaggtgtcttttttatttgattagta-tagcttatttttggt----ttgtttatggcatg-ctatgtatgtagGAGAAATGGCTGAAT---CCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGATCAAGAGGCAAGAGGAATGGGCATTGGCCAAGAAAGATGAAGCTGTAGC
          ||| ||||   | || |||||| |   ||   |   | |  || ||  |  |  || | | |||  | ||      ||   | ||   ||  | |     |   ||| |||| ||||      |||||||| |||||||| || ||| | ||||||  ||||||| | ||||||||||| |||||||||||  | |||   |  ||
gtaagttccatctttgatctgccat-tgttcattgagtctctgcgttttgcttaatccgccttatagttgtttagatctgagaatatttcgtctgatttgattgttcgaatgacagAGATGGGTGAAGAAGTGAAGGTAGTTGTTCCAGAATCAGTGTTGAAGAAGCGCAAGAGGGAGGAGGAATGGGCGTTGGCCAAGAAGCAAGAACTCGATGC
















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|86036885|gb|DR332640.1|DR332640
EST:     TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAATGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: TTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036872|gb|DR332627.1|DR332627
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGAAGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036886|gb|DR332641.1|DR332641
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036883|gb|DR332638.1|DR332638
EST:     TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: TTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036875|gb|DR332630.1|DR332630
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|116408124|gb|EG450716.1|EG450716
EST:     CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036881|gb|DR332636.1|DR332636
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036876|gb|DR332631.1|DR332631
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036880|gb|DR332635.1|DR332635
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036879|gb|DR332634.1|DR332634
EST:     TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: TTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036882|gb|DR332637.1|DR332637
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036873|gb|DR332628.1|DR332628
EST:     TTCCTCTTCATCTCAA                         GAGAAWTGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: TTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036877|gb|DR332632.1|DR332632
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|152035827|gb|BP862892.2|BP862892
EST:     CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAA                         GAGAAATGGGTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|86036878|gb|DR332633.1|DR332633
EST:     CGCACACTATCTTTTCCTCTCACTCAGAC-----TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: CGCACACTATCTCTTCCTCTCTCTCAGACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA
EST: gi|163995891|gb|ES003895.1|ES003895
EST:     GACGAGATTTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAG
genomic: GACGAGATTTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAG
EST: gi|86036874|gb|DR332629.1|DR332629
EST:     TTCCTCTTCATCTCAA                         GAGAAATGGCTGAATCCAAGGTAATGGTTCCAGAGTCTGTGCTAAAGAAGA
genomic: TTCCTCTTCATCTCAAgtaagcttct ... atgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatttgattagtatagcttatttttggtttgtttatggcatgctatgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGATCAAGAGGCAAGAGGAATGGGCATTGGCCAAGAAAGATGAAGCTGTAGC
  atttgat  putative branch site (score: 5)
            tatagcttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttctctgtgattaacaatctgttcaatttctcaaaggtgtcttttttatttgattagtatagcttatttttggtttgtttatggcatgctatgtatgtagGAGAAATGGCTGAATCCAAGGTAGTGGTTCCAGAGTCTGTGCTAAAGAAGATCAAGAGGCAAGAGGAATGGGCATTGGCCAAGAAAGATGAAGCTGTAGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
ttctctg
- - - - - - aacaatc
- - - - - - - - - - - - - - tctcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtttgt