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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcaacttgtgagcagcattaaatatgtatagccaagttgtgtaaattctgtttgttgtaaaattgctttgtggcagttttcataggctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT

Basic information

species Glycine max
transcript GLYMA17G05530.4
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G05530.2 (Glycine max), 3'ss of exon 10
lower sequence: Vv11s0016g00700.t01 (Vitis vinifera), 3'ss of exon 10
---gcaacttgtgagcagcattaaatatgtatagccaagttgtgtaaattctgtttgttgtaaaattgctttgtggca---gttttcatag-gctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT
      | || |    | ||  | | |  ||| | || | | || | |     | | ||| |||||| |||| || ||   | |||| ||      |  |||||||||||||||| ||||| ||||| | |||||||||| | |||   || ||| |||||||||||||| ||||||||||||| ||||| ||||| ||||||||||
attattatttttata-atcagaacacaactatgggca-gctctgaaga----atgttttgcaaaatt-ctttctgccattagctttcttattaacttataattgcagGTTACTTCAGTTGACCTCCACCGACATTTTCATGCACTTGGCGCTGGAGCTATTGAAGATGTTCGGGTGCAACGAGATAAAGGCTTTGGTTTTGTGAGAT
















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|208267978|gb|GE072949.1|GE072949
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCC
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCC
EST: gi|10709423|gb|BF009147.1|BF009147
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|10709102|gb|BF008826.1|BF008826
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|163922870|gb|EH038800.1|EH038800
EST:     TCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: TCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|15285660|gb|BI469551.1|BI469551
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|11687387|gb|BF595063.1|BF595063
EST:     AGACGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAC                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|163921601|gb|EH038699.1|EH038699
EST:     TCCTC-ATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: TCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|6454389|gb|AW185072.1|AW185072
EST:     TCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: TCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|13312169|gb|BG405829.1|BG405829
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|193493686|gb|FK458868.1|FK458868
EST:     ATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: ATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|7925242|gb|AW831268.1|AW831268
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|26058248|gb|CA801162.1|CA801162
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|9563980|gb|BE473489.1|BE473489
EST:     CTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: CTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|208146424|gb|GD946261.1|GD946261
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|6072359|gb|AW101746.1|AW101746
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|24136117|gb|BU926627.1|BU926627
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|5175311|gb|AI759644.1|AI759644
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTGCATCAACAT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACAT
EST: gi|193488603|gb|FK453584.1|FK453584
EST:     ATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: ATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|6454619|gb|AW185302.1|AW185302
EST:     AGAAGAATCCTCAATATACCACTGGTTATGTTGGCAATCTTGCTTCAGAG                         GTTTCTTCTGT-GATCTTCATCA-CATTT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTT
EST: gi|193687566|gb|FK629225.1|FK629225
EST:     ATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: ATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|207745466|gb|GD714028.1|GD714028
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|208082894|gb|GD882160.1|GD882160
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|208309506|gb|GE103368.1|GE103368
EST:     ATACCACTGCTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: ATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|208189187|gb|GD984403.1|GD984403
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|208325993|gb|GE119703.1|GE119703
EST:     AGAGGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACAATTTTAACATTCTCTTAAT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACA-TTTT--CATTCTCTTAAT
EST: gi|193653976|gb|FK596964.1|FK596964
EST:     ATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: ATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|21637806|gb|BM107961.1|BM107961
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
EST: gi|193716792|gb|FK650752.1|FK650752
EST:     ATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTAGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAAC
genomic: ATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCT-GTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAAC
EST: gi|19053974|gb|BM732641.1|BM732641
EST:     AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAG                         GTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT
genomic: AGAAGAATCCTCAATATACCACTGTTTATGTTGGCAATCTTGCTCCAGAGgcaaggataa ... gaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctgtttgttgtaaaattgctttgtggcagttttcataggctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT
     tttgttgtaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcaacttgtgagcagcattaaatatgtatagccaagttgtgtaaattctgtttgttgtaaaattgctttgtggcagttttcataggctgtgaaattgcagGTTACTTCTGTTGATCTCCATCAACATTTTCATTCTCTTAATGCCGGAACTATTGAAGATGTTAGGGTGCAACGAGACAAAGGTTTTGGGTTTGTGAGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG