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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttttgagcactataaatttgttttgttgtatcttatttcaatgtttttctgtagattttctttctagtgatttcactctaatttttgccttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCCTATTTGAACACATATGACGGCCGTACCATCCGCTATCCTGACCCACTAA

Basic information

species Glycine max
transcript GLYMA03G06440.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G06440.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0004g07150.t01 (Vitis vinifera), 3'ss of exon 4
gcttttgagcactataaatttgttttgttgtatcttatttcaatgttt-ttctgtagattttctttctagtgatttcactc--taatttttgcc-ttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCCTATTTGAACACATATGACGGCCGTACCATCCGCTATCCTGACCCACTAA
    |  ||    | ||   | || | || | |     | || | | |  |     |||||      |   | | | |  |  |  | |||| | || || ||||||||||||||||||||  | ||||| || ||||| || ||||| ||||| ||| | ||||| ||||| || || ||||||||||| ||||| || || |
----tcaagatagaaaagaatcttcttttttgtggacgtgcagtttgtactaaactgatttaggcatttaggctctgatgcaatgttatttgtcattcttgcagTTTAAGCTCTGCAAGGTGAGGTCTGTGCAGTTTGGACAGAAGGGAATCCCATATCTCAACACTTATGATGGGCGAACCATCCGCTACCCTGATCCTCTGA
















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|298188907|gb|HO035600.1|HO035600
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|151396175|gb|EV266052.1|EV266052
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|192300483|gb|FG987910.1|FG987910
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|7284412|gb|AW597004.1|AW597004
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGGTCAATTTGGGCAAAAGGGCATTCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|9203665|gb|BE329889.1|BE329889
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|298196174|gb|HO044565.1|HO044565
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|9986822|gb|BE660930.1|BE660930
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|298190510|gb|HO032631.1|HO032631
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|13789053|gb|BG651644.1|BG651644
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCAGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|298186402|gb|HO037035.1|HO037035
EST:     ACACGAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|31310120|gb|CD395323.1|CD395323
EST:     GTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: GTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
EST: gi|17401982|gb|BM178764.1|BM178764
EST:     ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAG                         TTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC
genomic: ACACAAAAGGTCGATTCCGTCTCCACTCTGTAAGGGACGAAGAGTCAAAGgtttgtctat ... cttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttctgtagattttctttctagtgatttcactctaatttttgccttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCCTATTTGAACACATATGACGGCCGTACCATCCGCTATCCTGACCCACTAA
                                ctctaat  putative branch site (score: 3)
                                      tttttgccttgtttc  CT-rich tract
                                 tctaattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttttgagcactataaatttgttttgttgtatcttatttcaatgtttttctgtagattttctttctagtgatttcactctaatttttgccttgtttcagTTTAAGCTCTGCAAGGTTCGATCTGTTCAATTTGGGCAAAAGGGCATCCCCTATTTGAACACATATGACGGCCGTACCATCCGCTATCCTGACCCACTAA

gcttttg
- - - - - - - - - - tgttttg
- - - - - - - - - - - - - - - - - - - - caatgtt
- - - - - - - - - - - - - - - - - - - - - - - - ttctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cactcta