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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cattatgttggattcataaaagatagctgtaattttcatctaacagtaatattaaagtgagactaacgttcttttataaaaaaacaaaaatctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 12
------cattatgttggattcataaaagatagctgtaattttcatctaacagtaatattaaagtgagactaacgttcttttataaaaaaacaaaaatctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG
         ||  |  | ||   | |  |      |  ||||  || ||   | ||   | |  | ||| |   |  |  | |       ||||  ||    | |||| || ||||| || |||||  ||||||| || |||   || ||||||||||| ||||| ||||||||||| || ||||| || |||||||| || || |
aatgatagctaaatgtgctttgcagataaacttgtttttttttttcaaatttttatgccatatggggacaattatcatcctctt------caaatttcatgtttagGGCATAGATGGTTCAAGAGTGGAGAAGGTTTTAGAAAACGTGCACATTGCAGCAAACAAGAACACAGTTCCTGGTGATGTTTCAGCTATGGTACCAGGAG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 4
-----catta----tgttggattcataaaagatagctgtaattttcatctaacagtaatattaaagtgagactaacgttcttttataaaaaaacaaaaatctctgt-cagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG
      || |    |||||| | |||  ||  ||  |||| | || | ||   | ||  |  ||||  |||   ||  | | |||| |           ||||||| |||||||||||||||||||||||| | |||||||||||||| ||||| |||| ||||||||||||||| ||||| ||||||||||| || ||||||||| |||
aaatatatgagagttgttggctccatttaatttatgtgtattatttagcttttattataa--aaaggaagagccactatttcttatga--------ttttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGTAGCTAACAAAAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 12
---------cattatgttggattcataaaagatagctgtaattttcatctaacagtaatattaaagtgagactaacgttcttttataaaaaaacaaaaatctctgt-cagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG
              |||||| | |||  ||  ||  ||||    |||| || |  | ||  ||||  |  |    |  | |||  ||        |   ||||||| |||||||||||||||||||||||| | |||||||||||||| ||||| |||||||||||||| ||||| ||||| ||||||||||| || |||||||||||||
aaatagataagagttgttggctccatttaatttatgtgta----tcatttagcttttattataaaaaggaagagccactatttctta------tgattttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTGGAATCTGTTCATATTGCAGCTAACAAGAACACCGTTCCTGGAGATGTGTCGGCCATGGTTCCTGGTG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 12
---------cattatgttggattcataaaagatagctgtaattttcatctaacagtaatattaaagtgagactaacgttcttttataaaaaaacaaaaatctctgt-cagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG
              |||||| | |||  ||  ||  ||||    | || ||||  | ||  ||||  |  |    | || |||  ||        |   ||||||| |||||||||||||||||||||||| | |||||||| ||||| ||||| |||| ||||||||||||||| ||||| ||||||||||| || ||||||||| |||
aaatatttgagagttgttggctccatttaatttatgtgta----ttatttaacttttattataaaaaggaagagccattatttctta------tgattttctctgttcagGGTATTGATGGCTCCAGAGTTGAAAAGGTGTTAGAATCTGTTCATATTGTAGCTAACAAAAACACTGTTCCTGGAGATGTGTCGGCCATGGTTCCTAGTG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 12
lower sequence: PP1S21_270V6.1 (Physcomitrella patens), 3'ss of exon 11
--------------------cattatgttggattcataaaagata-gctgtaattttcatctaacagtaatattaaagtgagactaacgttct--tttataaaaaa--acaaaaatctctgt-cagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG
                    |    |  ||   ||| |      | | | ||||||||  | |  |  | ||||||  | |||||   || ||  | |   |  ||         ||  |||  ||||| | || || || || ||  ||   ||| ||||    |  ||||||||||| ||||| ||||| ||||||||||||||||| ||  |||| ||||| |
gtgtattctgcaaactcttcctcagtactgttatcacatgttccatgttctaattttctaccagtatgactattaat-taagactg-tgtcctgatctgcgatgaatggttcttgtcattgtgtagGGTGTGGACGGTTCAAGGGTGGAGCGAGTGATGGAGCTTGCCCACATTGCAGCAAACAAGAACACTGTTCCAGGAGATGTGTCTGCATTGGTACCTGGAG

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|208213023|gb|GE009184.1|GE009184
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGGATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|193351009|gb|FK315773.1|FK315773
EST:     TTCTGGTGGAACTGAGAATCATCTACTTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTCTGGTGGAACTGAGAATCATCTACTTTT-GGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|207828088|gb|GD797979.1|GD797979
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|207781497|gb|GD754020.1|GD754020
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAAAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGT
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGT
EST: gi|208197654|gb|GD998875.1|GD998875
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|208201733|gb|GE000507.1|GE000507
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGT-CACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|193427342|gb|FK396168.1|FK396168
EST:     GGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: GGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|208337743|gb|GE135181.1|GE135181
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTT
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTT
EST: gi|208324639|gb|GE120634.1|GE120634
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|207731953|gb|GD705634.1|GD705634
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|208290230|gb|GE084492.1|GE084492
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|22931030|gb|BU548169.1|BU548169
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|16346437|gb|BI972032.1|BI972032
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|208322012|gb|GE125973.1|GE125973
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|193385890|gb|FK351112.1|FK351112
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|208134534|gb|GD930927.1|GD930927
EST:     TACTCTTGGTGAATTCTTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TACTTTTGGTGAA-TC-TGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|16348582|gb|BI974177.1|BI974177
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCA
EST: gi|208218304|gb|GE020032.1|GE020032
EST:     TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAG                         GGTATTGATGGCTCCAGAGTTCA
genomic: TTTCTGGTGGAACTGAGAATCATCTACTTTTGGTGAATCTGAAGAGCAAGgtaaactaca ... tctctgtcagGGTATTGATGGCTCCAGAGTTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatattaaagtgagactaacgttcttttataaaaaaacaaaaatctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG
               gactaac  putative branch site (score: 1)
                                             tctctgtc  putative PPT
                  taacgttcttttataa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cattatgttggattcataaaagatagctgtaattttcatctaacagtaatattaaagtgagactaacgttcttttataaaaaaacaaaaatctctgtcagGGTATTGATGGCTCCAGAGTTCAGAAGGTGTTGGAATCAGTTCACATTGCAGCTAACAAAAACACAGTTCCAGGAGATGTGTCCGCTATGGTTCCTGGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - atgttgg
- - - - - - - - - - - - agctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaaa