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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattttgtttgtcagatgtttggagttggctctcaatttctattctatattaatatttcttcatataggcatactaatgcttaaatgtgaaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTCAATCAGATGGCTGAGCAGCTTCAGAAAACTTTTCAAGGAGCTCCACAAG

Basic information

species Glycine max
transcript GLYMA06G47830.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G17390.1 (Arabidopsis thaliana), 3'ss of exon 3
gaattttgtttgtcagatgtttggagttggctctcaatttctattctatattaatatttcttcatataggcatactaatgcttaaatgtgaaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTCAATCAGATGGCTGAGCAGCTTCAGAAAACTTTTCAAGGAGCTCCACAAG
       ||  ||    | ||  | ||      ||| |   || || |   |   |||| ||| | |     |   | || ||   |      |    |||||||||||||||||||||||||||| || ||||| |||||||| || || || ||| | |||||||||||||||| | || | | |   |   | || |
-------gtaagttctcttttgtgggtgtatgatcattgaatagtcaaaggttggattttttcttgtg----tttgattggtttgtt------tattcagGATCCAAGTATCAAGGAATTGGCTGAGCAAATAGCTAAAGATCCTTCATTTAACCAGTTAGCTGAGCAGCTTCAGAGATCTGTGCCAACCGGATCTCATG

upper sequence: GLYMA06G47830.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0038g04270.t01 (Vitis vinifera), 3'ss of exon 3
gaattttgtttgtcagatgtttggag--ttggctctcaatttctattctata-ttaatatttcttcatatag-gcatactaatgcttaaatgtgaaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTCAATCAGATGGCTGAGCAGCTTCAGAAAACTTTTCAAGGAGCTCCACAAG
     | |||  |||  |  |   ||  ||     |   |||  |   |  | ||||    | ||  | ||  ||  | |||||  ||       |   ||||||||||||| || || ||||| || |||||||| |||||||||||  | ||||| |||||||| |||||||| || || |||||||| || ||  ||   |
----gtagttcatcatttcctcaaagaattattgtttgtttttcaaagttcaattaactagttttagtttattgctcattaatgtctatggaatgataccatagGATCCAAGCATTAAAGAATTAGCAGAACAGATTGCAAAAGATCCTGCATTCAACCAGATGGCAGAGCAGCTCCAAAAGACTTTTCATGGTGCAGCAGTTG
















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|192309988|gb|FK002512.1|FK002512
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|209715174|gb|BW665651.1|BW665651
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|10843162|gb|BF066475.1|BF066475
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|209712540|gb|BW684130.1|BW684130
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|193523866|gb|FK477887.1|FK477887
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|10710560|gb|BF010278.1|BF010278
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|10709138|gb|BF008862.1|BF008862
EST:     GGCCTCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|254335876|gb|GR847404.1|GR847404
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|208084739|gb|GD882715.1|GD882715
EST:     GCATCCAGGCAACCCTTTTGATTCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGNTCCATCGTTC
genomic: GCATCCAGGCAACCCTTTTGAT-CTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|5605985|gb|AI900083.1|AI900083
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
EST: gi|151407493|gb|EV277308.1|EV277308
EST:     GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAAT                         GATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC
genomic: GGCATCCAGGCAACCCTTTTGATCTCTCAGCAATGTCTGGTCTGCTCAATgtaaatcatt ... aaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctatattaatatttcttcatataggcatactaatgcttaaatgtgaaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTCAATCAGATGGCTGAGCAGCTTCAGAAAACTTTTCAAGGAGCTCCACAAG
                           tactaat  putative branch site (score: 1)
     ttaatatttcttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattttgtttgtcagatgtttggagttggctctcaatttctattctatattaatatttcttcatataggcatactaatgcttaaatgtgaaatgcatagGATCCAAGTATCAAGGAATTGGCTGAACAGATAGCAAAAGATCCATCGTTCAATCAGATGGCTGAGCAGCTTCAGAAAACTTTTCAAGGAGCTCCACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT