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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcgtgtcctgttcacttgttagttctctactgttttacgaagtactcaattacagttatttccccggatttgttattagagctcttgtaattgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAGCAAGCTGTAGCTGGTGATGTTGTCTCCTTACCTAAATATAAGGGTATGC

Basic information

species Glycine max
transcript GLYMA03G14780.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G14780.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g01700.t01 (Vitis vinifera), 3'ss of exon 1
----ctcgtgtcctgttcacttgttagttctctactgttttacgaagtac-tcaattacagttatttccccggatttgttattagagctcttgtaattgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAGCAAGCTGTAGCTGGTGATGTTGTCTCCTTACCTAAATATAAGGGTATGC
     | |  ||||    |     ||  | | |||||| ||  || |||  |   || |  |  | |    | ||   | |  || | | ||    ||||   || | ||||| ||||||||||||||||| ||||| ||||||||||| |||||| ||||||| || || ||||  ||  ||||||| ||||||| |||| |||
ttaatttggatccttgaaataaactacct-tgtactgtctt--gatgtaaattggttcctatggtgttatggcatccctga--agtgtttttaattttgatgcagATCTGTACAATTCCTTTGGATACTGCTAAAGTTAGGCTTCAGCTCCAAAAGAAAGCTGTTGCAGGAGATGGAGTGGCCTTACCAAAATATAGGGGTCTGC
















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|21994526|gb|BQ786054.1|BQ786054
EST:     CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|17022665|gb|BM093699.1|BM093699
EST:     CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|7685497|gb|AW756145.1|AW756145
EST:     CTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|208086743|gb|GD879889.1|GD879889
EST:     CTTCGGAAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CTTCGGAAAAA-TCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|209724656|gb|BW677736.1|BW677736
EST:     CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|24136062|gb|BU926572.1|BU926572
EST:     CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|151397018|gb|EV266891.1|EV266891
EST:     CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|213595388|gb|DB966526.1|DB966526
EST:     CCTTCGGAAAAATCCTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|7685710|gb|AW756358.1|AW756358
EST:     CTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|151396786|gb|EV266659.1|EV266659
EST:     CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
EST: gi|18734274|gb|BM528089.1|BM528089
EST:     CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAG                         GTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG
genomic: CCTTCGGAAAAATCTTTGCCAGCAGTGCTTTCTCTGCATGTTTCGCTGAGgtcatttgca ... attgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctcaattacagttatttccccggatttgttattagagctcttgtaattgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAGCAAGCTGTAGCTGGTGATGTTGTCTCCTTACCTAAATATAAGGGTATGC
                                        ttgtaattgaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctcgtgtcctgttcacttgttagttctctactgttttacgaagtactcaattacagttatttccccggatttgttattagagctcttgtaattgaaatagGTGTGTACTATTCCTTTGGATACTGCCAAAGTGAGGCTTCAGCTTCAAAAGCAAGCTGTAGCTGGTGATGTTGTCTCCTTACCTAAATATAAGGGTATGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - tgtcctg
- - - - - - -cacttgt
- - - - - - - - - - - - - tctactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatttg