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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctactacattttgaaacctttagcattgggtttaagggagatcttttatggggttttatatattatattatgttctatgtctgaatgtttgtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAAAGCATAATGAGTGAAGTCAGAACGAGTTCTGGGATGTTTCTCAACAAGG

Basic information

species Glycine max
transcript GLYMA13G04940.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g27340.2 (Oryza sativa), 3'ss of exon 2
ctactacattttgaaacctttagcattgggtttaagggagat-cttttatggggttttatatattatattatgttctatgtctgaatgtttgtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAAAGCATAATGAGTGAAGTCAGAACGAGTTCTGGGATGTTTCTCAACAAGG
           || |  || | ||||   | |  |    |   | ||   ||    || |   | ||| |   ||     |  ||   |||||      |||| |||||||||||||||||||| |||||||| || |||||||| || || ||| | ||||| || ||  | || || || || ||||| ||| | ||| 
------gtgagtgtacactgtggcatcccgctcgatctcgccgcattcggggaaccttttgggtaatagtggattg---attcga---tttgt------agGCGAAGGACAAGCTGGAGAAGTCGATGGTGGCGGACAACGAGTCCGGGAAGAGCGTCATGAGCGAGGTGCGGACCAGCTCCGGCATGTTCCTCGAGAAGA

upper sequence: GLYMA13G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G520535_T01 (Zea mays), 3'ss of exon 2
ctactacattttgaaacctttagcattgggtttaagggagatcttttatggggttttatatattatattatgttctatgtctgaatgtttgtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAAAGCATAATGAGTGAAGTCAGAACGAGTTCTGGGATGTTTCTCAACAAGG
     |      ||  |     | ||||| ||   | ||  |||  | |||    ||  ||  |   ||   ||   ||| ||| || |||  |     ||||||||||||||||||||||||||||||||| ||||||||||| ||||| ||  |   |||||| ||  | || || || || ||||| ||| | | | 
--gtgagtgccagaggctgggtggattggctt---gtgatgtctgctttggttcgttccatcgttggttg-atttggtgtttgattggttgaaa-----gGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCCGATAACGAGTCCGGTAAGAGTGTCCAGAGTGAGGTGCGCACCAGCTCCGGCATGTTCCTCGAGAGGA

upper sequence: GLYMA13G04940.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G168506_T02 (Zea mays), 3'ss of exon 2
ctactacattttgaaacctttagcattgggtttaagggagatcttttatggggttttatatattatattatgttctatgtctgaatgtttgtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAAAGCATAATGAGTGAAGTCAGAACGAGTTCTGGGATGTTTCTCAACAAGG
     |      ||  |     | ||||| ||   | ||  | |  | ||     ||   || |   ||   |||  ||| ||| || |||       |||||||||||||||||||||||||||||||||| || ||| |||| ||||| ||  |   |||||| ||  | || ||||| || ||||| ||| | ||| 
--gtgagtgcccgaggctgggtggattggctt---gtgatgtatgctttgattcgttggttagttggttg-attcggtgtttgattggttga------agGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCGGACAACAAGTCCGGTAAGAGTGTCCAGAGTGAGGTGCGCACCAGTTCCGGCATGTTCCTCGAGAAGA

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|298189073|gb|HO037476.1|HO037476
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|192303526|gb|FG995932.1|FG995932
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|298195533|gb|HO043924.1|HO043924
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAGTGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|298175821|gb|HO018418.1|HO018418
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|192298241|gb|FG991717.1|FG991717
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|151411869|gb|EV281680.1|EV281680
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|213603274|gb|DB970395.1|DB970395
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|120491083|gb|EH219250.1|EH219250
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|192298016|gb|FG993250.1|FG993250
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|151394021|gb|EV263892.1|EV263892
EST:     TCTACAGGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|254330721|gb|GR841986.1|GR841986
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|23062388|gb|BU578509.1|BU578509
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|151407677|gb|EV277492.1|EV277492
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|151395404|gb|EV265281.1|EV265281
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|120530553|gb|EH258686.1|EH258686
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAA
EST: gi|213611820|gb|DB958886.1|DB958886
EST:     TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTG                         GCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGAATAACGAGTCTGGTAA
genomic: TCTACAAGGGCTTTTTATCCGATGAAGAATGTGATCATTTGATAACTCTGgttagatttt ... gtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAG-ATAACGAGTCTGGTAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggggttttatatattatattatgttctatgtctgaatgtttgtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAAAGCATAATGAGTGAAGTCAGAACGAGTTCTGGGATGTTTCTCAACAAGG
        ttttatatattatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctactacattttgaaacctttagcattgggtttaagggagatcttttatggggttttatatattatattatgttctatgtctgaatgtttgtgatattagGCCAAGGACAAGCTGGAGAAGTCTATGGTGGCAGATAACGAGTCTGGTAAAAGCATAATGAGTGAAGTCAGAACGAGTTCTGGGATGTTTCTCAACAAGG

- -ctacatt
- - - - - -tgaaacc
- - - - - - - - - - - - - - - - - - - - - - - - -ggggttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctatgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgaatgt