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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgcctgctgagttcttctgcttgtgttattttcttttttatggcattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG

Basic information

species Glycine max
transcript GLYMA15G05620.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G122039_T02 (Zea mays), 3'ss of exon 1
---gctgcctgctgagttcttctgcttgtgttattttcttttttatggcattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG---------------
    ||||     |    |    |    |   || || |         |  | | ||||  |   |  | |||  |  | |    || |||   | ||   ||||  |||||||||| |||||||||||||| ||||||||| ||    ||||| ||  ||||||||||| || |    |||||  ||               
ttcactgcacaacgg--ccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctct-atctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAGGTCTGCCTCCTTGGA

upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G122039_T07 (Zea mays), 3'ss of exon 1
gctgcctgctga--gttcttctgcttgtgttattttcttttttatggcattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG
  |  ||||  |  |  |    |    |   || || |         |  | | ||||  |   |  | |||  |  | |    || |||   | ||   ||||  |||||||||| |||||||||||||| ||||||||| ||    ||||| ||  ||||||||||| || |    |||||  ||
-ttcactgcacaacggccggtcgtcactagaatgttttgaaccgctcccctttttcctcctgtctcaagttccatgctttcctaatgttgctct-atctcagGGAGGACGAGGAACTTGTTGATCAGAAGAAATATCTTGAGGAACGATGCAAGCCGCAATGTGTAAAATCACTTTACGAATATGAG

upper sequence: GLYMA15G05620.1 (Glycine max), 3'ss of exon 1
lower sequence: AT2G01090.2 (Arabidopsis thaliana), 3'ss of exon 2
---gctgcctgctgagttctt-ctgcttgtgttattttcttttttatggcattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG
         ||||  ||  |   |      ||| | ||| ||  | | |  | ||   |||    |||  ||||  |  |  | |    | || || |||  ||| | || || ||   |||||||||||| |||||  |||| || |||||||||||||||||||| || ||| |||| ||||| |||
aacaaaaattgctatgtcatagttatgaacgttttattcgttcct-tagtttgcttatctaacctttgattttccatcctactcga---tggttataattacagGCCAGAAGAAGATGTTGTTGATCAGAAAAGATACTTTGAGGAATCTTGCAAACCAAAATGTGTGAAGCCACTACTTGAATATCAG

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|298198142|gb|HO039681.1|HO039681
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|7639289|gb|AW733615.1|AW733615
EST:     CCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: CCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|58014473|gb|CX701215.1|CX701215
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|193393950|gb|FK358081.1|FK358081
EST:     AAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|14999290|gb|BI320299.1|BI320299
EST:     CACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: CACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|193431244|gb|FK396850.1|FK396850
EST:     AAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|18733830|gb|BM527835.1|BM527835
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|7639244|gb|AW733571.1|AW733571
EST:     CCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: CCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|20814521|gb|BQ298999.1|BQ298999
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|7146375|gb|AW508297.1|AW508297
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|17402023|gb|BM178805.1|BM178805
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|22931573|gb|BU548712.1|BU548712
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|10848067|gb|BF070624.1|BF070624
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|151400909|gb|EV270723.1|EV270723
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|13251785|gb|BG362688.1|BG362688
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|18848956|gb|BM568066.1|BM568066
EST:     CTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: CTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|6914391|gb|AW395921.1|AW395921
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|151410688|gb|EV280503.1|EV280503
EST:     AAACCCAAACAACAGCTCCACGGACCACACCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|18726815|gb|BM523771.1|BM523771
EST:     CTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: CTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|18848720|gb|BM567832.1|BM567832
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|254315068|gb|GR830061.1|GR830061
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|151401498|gb|EV271312.1|EV271312
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
EST: gi|23734278|gb|BU765362.1|BU765362
EST:     AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAAT                         GGCTGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA
genomic: AAACCCAAACAACAGCTCCACGGACCACCCCTACTGCTCTGCTCTGCAATgtaagcctcc ... atgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG
          tatttattgcatttca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgcctgctgagttcttctgcttgtgttattttcttttttatggcattctctcctatttattgcatttcatttatgtttggattttgtcatgattctagGGCCGACGAGGAACCTGTTGATCAGAAGAGATATCTTGAAGAGTCTTGCAAACCAAAATGTGTAAAACCATTACTGGAATACCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - -ctgctga
- - - - - - - -cttctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgtttg