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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgcatgtggatatggatattgcaacagaatttatttcattttcttaaaatgttatttctttgtgtgatcatcctaattaatacttgtataaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGACCATTGGGAATAGTCTGTTTCCAAACAGCAAAGGATA

Basic information

species Glycine max
transcript GLYMA08G15340.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G15340.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 10
---------gctgcatgtgg-atatggatattgcaacagaatttatttcattttcttaaaatgttatttctttgtgtgatcatcctaattaatacttgtataaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGACCATTGGGAATAGTCTGTTTCCAAACAGCAAAGGATA
          || ||  |   || | | ||  ||||||  ||| || |  ||  ||  || | | ||||      |||| |||    || ||  ||||| |  |  |||||| || |||||||||||||| |||||||| ||||| ||| | ||||| ||||| || || || ||| ||||| | ||||||||||| || |||||||| |
ctcacaactcctccacctctcattttgtta--gcaacacgatt-atgtggttacctagaactctgatttg--caagtgaacattt--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|27426694|gb|CA938214.1|CA938214
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|209699016|gb|BW656131.1|BW656131
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|6724429|gb|AW308828.1|AW308828
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAA                         GATGCTGAGAAGCATCTCTCAGATATAGTTGTGTCTAAAGCGCTG
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTG
EST: gi|9903102|gb|BE612070.1|BE612070
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|23064146|gb|BU578919.1|BU578919
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|7640049|gb|AW734358.1|AW734358
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|16347022|gb|BI972617.1|BI972617
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|151409280|gb|EV279088.1|EV279088
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|15204177|gb|BI426945.1|BI426945
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|14990230|gb|BI315903.1|BI315903
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|209725253|gb|BW672728.1|BW672728
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
EST: gi|17022111|gb|BM093145.1|BM093145
EST:     CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAG                         GATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA
genomic: CAAGAATTACATTGAAGAGACTTGCAGAGCTTTTGTGCCTCAGTGTACAGgtttgtgatt ... taaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaaaatgttatttctttgtgtgatcatcctaattaatacttgtataaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGACCATTGGGAATAGTCTGTTTCCAAACAGCAAAGGATA
                              taattaatacttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gctgcatgtggatatggatattgcaacagaatttatttcattttcttaaaatgttatttctttgtgtgatcatcctaattaatacttgtataaaattcagGATGCTGAGAAGCATCTCTCAGATATGGTTGTGTCTAAGGCGCTGGTGGCAAAGATTGATAGACCATTGGGAATAGTCTGTTTCCAAACAGCAAAGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- tgcatgt
- - - - - - - - - - -tgcaaca