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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgcatgcgaatatggatgttgcaacggaatttatttcattttcttaaaatgttatttctttgtttgattatcctaattaatacttgtgtaaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGGCCAATGGGGATAGTCTGTTTCCAAACAGCAAAGGATA

Basic information

species Glycine max
transcript GLYMA05G32030.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32030.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 10
-----gctgcatgcgaatatggatgttgcaacggaat--ttatttcattttcttaaaatgttatttctttgtttgattatcctaattaatacttgtgtaaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGGCCAATGGGGATAGTCTGTTTCCAAACAGCAAAGGATA
         | | |   | |   | |   | |   |   |||| |  ||  ||  || | | ||||    ||  ||  ||    || ||  ||||| |  |  |||||| || |||||||||||||| |||||||| ||||| ||| | ||||| ||||| || || |||||||||||  | ||||||||||| || |||||||| |
ctcacaactcctccacctctcattttgttagcaacacgattatgtggttacctagaactctgatttgcaagt--gaacattt--atgaa--cttgt-tccatctcagGAAGCCGAGAAGCATCTCTCGGATATGGTCGTGTCCAAGTCACTGGTTGCAAAAATCGACAGGCCAATGGGAGTCGTCTGTTTCCAGACGGCAAAGGACA
















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|151412403|gb|EV282215.1|EV282215
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGTGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|254341095|gb|GR854823.1|GR854823
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|13789644|gb|BG652235.1|BG652235
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|254341094|gb|GR854822.1|GR854822
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|151394588|gb|EV264459.1|EV264459
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|18734862|gb|BM528428.1|BM528428
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCG
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCG
EST: gi|193487785|gb|FK452766.1|FK452766
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCAT
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCAT
EST: gi|21601284|gb|BQ611615.1|BQ611615
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|151409910|gb|EV279718.1|EV279718
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|192309223|gb|FG999450.1|FG999450
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|22524861|gb|BU083672.1|BU083672
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|8827475|gb|BE211205.1|BE211205
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTATACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaatgttatttctttgtttgattatcctaattaatacttgtgtaaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGGCCAATGGGGATAGTCTGTTTCCAAACAGCAAAGGATA
                              taattaatacttgtgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgcatgcgaatatggatgttgcaacggaatttatttcattttcttaaaatgttatttctttgtttgattatcctaattaatacttgtgtaaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGGCCAATGGGGATAGTCTGTTTCCAAACAGCAAAGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG