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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

Basic information

species Glycine max
transcript GLYMA08G46500.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55160.2 (Arabidopsis thaliana), 3'ss of exon 2
tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
                      | | |   | |   ||   ||  |||     | | |  ||  |    |  ||    || ||  ||   | ||||||||||||||||||| || ||||||||||| || ||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||
---------------------gtttttggtattgagaa--aatcgtatataatactcttcttgaag---taacaatcattggtaattt-ttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
lower sequence: AT5G55160.1 (Arabidopsis thaliana), 3'ss of exon 1
-----tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
     ||||   ||      |  |     | |    || | |    ||  |||     | | |  ||  |    |  ||    || ||  ||   | ||||||||||||||||||| || ||||||||||| || ||||||||||||||||| ||||| |||||||| |||||||| ||||| ||||| ||||| ||||||||||
gttggtacttggttggttatagatacagtttttggtat-tgagaaaatcgtatataatactcttcttgaag---taacaatcattggtaattt-ttcttgtgtagGATGGTAATGAAGTCTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAAAAACTGATGAATGCTTACTGTGACCGTCAGTCTGTGGATTTCAACTCAATTG

upper sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
lower sequence: AT4G26840.1 (Arabidopsis thaliana), 3'ss of exon 1
----tactatctttaacccaactgattatctcacaatataaat-ttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
    |   |  ||    ||||  ||    |     || ||  | || ||| ||  | |    ||| ||    || ||  || || | |   ||  | || | |||||||| || ||||||||||||||||| || |||||||||||||||||||| || |||||||| |||||||| || |||||||| ||  | ||||| ||||
actctttcaggttactaccaaaagagagccatgtgatttagttattgtttcatatgcgg---tctctaacgtttattgttccttctata--tgtttgttttatagGATGGAAACGAGGTTTTCTTTAGGATCAAGAGAAGCACTCAGCTCAAGAAGCTGATGAATGCTTACTGTGACCGGCAATCTGTGGACATGAACTCCATTG

upper sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0186g00020.t01 (Vitis vinifera), 3'ss of exon 1
--------------tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
              | || | ||     |||||  |    |  | ||        |    |   | |||||  |||  ||| |||| ||   ||||||||||         ||||||||||| ||||| ||||||||||| ||||||||||| ||| |   ||| ||||||  ||| || |||||||| || || || || || ||||| ||||
atggatgactctcctcctgttttcttttcaactcctagcattcccattc--ccccaccccacaagtgaatt--tttgtaaaatttttat---tttgtggttg-------catagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTATTGTGATCGACAGTCAGTGGAGTTAAACTCCATTG

upper sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0059g01310.t01 (Vitis vinifera), 3'ss of exon 1
---tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
     | |  | |||       || ||    |  || |   |||    | ||   |  || ||  ||||  |    |   | | || ||    |||  || ||||||| ||||| |||||||| ||||| ||||||||||| ||||| ||||| || |||||||| || ||||| || |||||||||||  | ||||| ||||
gggagcaagttctaagaatttggactaaa--aatatctctgtttgcagtttgctaggtttcctggacaagatgacgaggatgt-gttgtgttttttattgcagGATGGGAATGAAGTTTTCTTCAGGATCAAAAGAAGCACACAGCTGAAGAAGCTCATGAATGCTTATTGTGACCGACAATCTGTAGACCTCAACTCGATTG

upper sequence: GLYMA08G46500.2 (Glycine max), 3'ss of exon 1
lower sequence: Vv00s0186g00080.t01 (Vitis vinifera), 3'ss of exon 1
tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
||       |    |   || ||   |  |||  |  |    |   ||    | |   |   |   | ||||  |    |  |  ||     |||||||||||||||| ||||| ||||||||||| ||||||||||| ||| |   ||| ||||||  ||| |||||||||||||| || || || || ||||| ||||
tatggatagttctgctcttgttttcttttcaacttccaccattcccatccttgtaccccacaagtgaatttttttaaaatgttcttttctggttgtgtagGATGGTAACGAGGTGTTCTTTAGGATCAAAAGAAGCACCCAGTTACGGAAGCTTATGTCTGCTTACTGTGATCGTCAGTCAGTGGAGTTAAACTCCATTG

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|209705640|gb|BW673597.1|BW673597
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|298185549|gb|HO030762.1|HO030762
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151401582|gb|EV271396.1|EV271396
EST:     AGGAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|213606787|gb|DB974320.1|DB974320
EST:     CAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCATTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: CAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|192314400|gb|FK008398.1|FK008398
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|254332811|gb|GR850061.1|GR850061
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|209720562|gb|BW675034.1|BW675034
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151413006|gb|EV282814.1|EV282814
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|254345516|gb|GR851678.1|GR851678
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|208085531|gb|GD881505.1|GD881505
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|254316463|gb|GR828000.1|GR828000
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151394557|gb|EV264428.1|EV264428
EST:     AGAAGCCTTCTGACCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151412622|gb|EV282434.1|EV282434
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151408444|gb|EV278252.1|EV278252
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|151412572|gb|EV282384.1|EV282384
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|209705641|gb|BW673598.1|BW673598
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
EST: gi|213600235|gb|DB955859.1|DB955859
EST:     AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAG                         GATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA
genomic: AGAAGCCTTCTGATCAAGGAGCACATATTAATCTCAAAGTCAAGGGCCAGgtctcaattc ... ttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG
                                      ggttgac  putative branch site (score: 4)
                                            cttttgt  CT-rich tract
        aatttctttacaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tactatctttaacccaactgattatctcacaatataaatttattttatgggggaatttctttacaaatttttcatctttttgtggttgacttttgtgtagGATGGTAATGAGGTTTTCTTTAGGATTAAAAGAAGCACTCAGCTCAAGAAACTTATGAATGCATACTGTGATCGTCAATCTGTAGATTTTAACTCAATTG

- - - - - - cccaact
- - - - - - - - - - - - - - - - - - - - - - - - gggggaa