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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtaatgagggattctgtgtttttaccttgtggattaataatgaaacttttggtgaaaaactttgaagttagctaatgctttatgtatggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGATCCTCGTCAGAGAAAACCAGACATTACAAAAGCAAAGGAATTGCTGGGAT

Basic information

species Glycine max
transcript GLYMA12G06980.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g16980.2 (Oryza sativa), 3'ss of exon 11
gatgtaatgagggattctgtgtttttaccttgtggattaataatgaaacttttggtgaaaaactttgaagttagctaatgctttatgtatggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGATCCTCGTCAGAGAAAACCAGACATTACAAAAGCAAAGGAATTGCTGGGAT
  |   ||||   || ||||      || |  |   |  ||        | |   ||  |  ||   |||||  |   ||||||          |||||| | || || ||| | ||     | |  |||  ||||||||||||||| |||||||||||||| || |||||||||||||| ||||||||| |  |||| |
-gtaagatgaat-atcctgttgccgaacatcat---tccatgggatgtttctgaatggcatgct---aagtttccc--tgctttt------accttgcagTTGATCAACCCAGAGGTTACCGTCACAATGACTGAGAACACTCCTGATGATCCTCGTCAGAGGAAGCCAGACATTACAAAGGCAAAGGAAGTTTTGGGGT

upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 12
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 9
gatgtaatgagggattctgtgtttttaccttgtggattaataatgaaacttttggtgaaaaactttgaagttagctaatgctttatgtatggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGATCCTCGTCAGAGAAAACCAGACATTACAAAAGCAAAGGAATTGCTGGGAT
               |     |||||    | |   || | | | ||  |    || | |||     |||| |  |  |   | |||     |  ||||||||||||| ||  | ||||||||||| ||||| |||||||| ||||| |||||  | ||||| ||||||||||| |  ||||| || ||| | || || |
--------------gttaacatttttgttatttcatttcaca-taaatgt----gtaacaaat----aagtaatgtcgtatataatgagaattgatgcagCTTATTAAACCGGACGTGGAGATAAAGATGGTAGAGAACACACCTGATGATCCAAGGCAGAGGAAACCAGACATAAGCAAAGCTAAAGAAGTTCTTGGTT

upper sequence: GLYMA12G06980.3 (Glycine max), 3'ss of exon 12
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 12
-gatgtaatgagggattctgtgtttttaccttgtggattaataatgaaacttttggtgaaaaactttgaagttagctaatgctttatgtat-ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGATCCTCGTCAGAGAAAACCAGACATTACAAAAGCAAAGGAATTGCTGGGAT
  ||  ||  | || |      |    |   | |  |||   | |  |  | ||  |      ||      ||    ||||||| |||  | | | |||||||| ||||||||  | |||| |||||| ||||| || ||||||||||| ||||| || ||||| |||||||||||| | || || || |||||| | ||||
gaattcaaacatggttgtgaaatacagaggatttcaatt--cagttgagttgttattttggctctgatggattgataaatgcttaatggctcgatgttgcagCTAATTAATCCTGAGGTGGTGATAAAAATGGTAGATAACACTCCTGATGATCCACGACAGAGGAAACCAGACATTTCTAAGGCTAAAGAATTGTTAGGAT

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|209714718|gb|BW674256.1|BW674256
EST:     ATGATTGAACTTGCTGAGAATGTGAAAGAG                         CTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
genomic: ATGATTGAACTTGCTGAGAATGTGAAAGAGgttagttgta ... ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
EST: gi|193521072|gb|FK478125.1|FK478125
EST:     GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAG                         CTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
genomic: GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAGgttagttgta ... ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
EST: gi|193616842|gb|FK571596.1|FK571596
EST:     GAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAG                         CTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
genomic: GAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAGgttagttgta ... ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
EST: gi|214004740|gb|DB985629.1|DB985629
EST:     ATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAG                         CTTAATAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
genomic: ATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAGgttagttgta ... ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
EST: gi|208182321|gb|GD980334.1|GD980334
EST:     GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAG                         CTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
genomic: GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAGgttagttgta ... ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
EST: gi|208205622|gb|GE006621.1|GE006621
EST:     GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAG                         CTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
genomic: GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAGgttagttgta ... ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
EST: gi|209703510|gb|BW656548.1|BW656548
EST:     GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAG                         CTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT
genomic: GCGAATTTACTATGATTGAACTTGCTGAGAATGTGAAAGAGgttagttgta ... ggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaacttttggtgaaaaactttgaagttagctaatgctttatgtatggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGATCCTCGTCAGAGAAAACCAGACATTACAAAAGCAAAGGAATTGCTGGGAT
                           agctaat  putative branch site (score: 3)
            aaaaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtaatgagggattctgtgtttttaccttgtggattaataatgaaacttttggtgaaaaactttgaagttagctaatgctttatgtatggttttgcagCTTATTAATCCAAAAGTGGAGATAAATATGGTTGAGAACACTCCTGACGATCCTCGTCAGAGAAAACCAGACATTACAAAAGCAAAGGAATTGCTGGGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA