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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttacattatatggaatattcaatccatccctgcattatttgctcttgcagtttaattttgccctcattctgaaatttgtaatctctctccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGCAATGCCTATAGGTGCCCACACAGTACTTGGTTTTCTTGCTGAACCCTTA

Basic information

species Glycine max
transcript GLYMA07G04680.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G04680.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv09s0002g00840.t01 (Vitis vinifera), 3'ss of exon 13
-ctttacattatatggaatattcaatccatccctgcattatttgctcttgcagtttaattttgccctcattctgaaatttgtaatctctctccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGCAATGCCTATAGGTGCCCACACAGTACTTGGTTTTCTTGCTGAACCCTTA
 |   | ||  ||     ||||       |  ||   ||      | ||    || | |||||    | |||||||  |||   | |   |     | |||||||||| | ||| ||||||||||| | |||||||||||||| || |||||||||||  | ||||| |||||  ||||| |||| ||||||||||| || 
tcaaaaaatagtaatacgtattactcttgtttctttcttgcccctttttatcatt-acttttgttggctttctgaagattgacctttggttgtttgtatagCAACATATTGTTCAGGGAGTTTTCTCTAATTTCTATGTGGAGGGTTCCAGCAATGCCAGTTGGTGCACACACTTTACTTAGTTTCCTTGCTGAACCTTTG
















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|15337755|gb|BI498411.1|BI498411
EST:     AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAG                         CAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC
genomic: AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAGgtaagtaatg ... ccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC
EST: gi|10845108|gb|BF071065.1|BF071065
EST:     AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAG                         CAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC
genomic: AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAGgtaagtaatg ... ccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC
EST: gi|193725821|gb|FK657721.1|FK657721
EST:     AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAG                         CAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC
genomic: AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAGgtaagtaatg ... ccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC
EST: gi|8283841|gb|BE021400.1|BE021400
EST:     AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAG                         CAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC
genomic: AATGTCAAAGATGTCAGTAAAAAGCTGCTTCTCCGAGCACTGATTCATAGgtaagtaatg ... ccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttgcagtttaattttgccctcattctgaaatttgtaatctctctccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGCAATGCCTATAGGTGCCCACACAGTACTTGGTTTTCTTGCTGAACCCTTA
      gtttaat  putative branch site (score: 4)
                                      tctctctccccctgt  putative PPT
     agtttaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttacattatatggaatattcaatccatccctgcattatttgctcttgcagtttaattttgccctcattctgaaatttgtaatctctctccccctgtagCAACATACTCTTCCGGGAGTTTTCTTTGATTTCTATGTGGAGAGTACCAGCAATGCCTATAGGTGCCCACACAGTACTTGGTTTTCTTGCTGAACCCTTA

- - - - - - - - - - - - tccatcc
- - - - - - - - - - - - - - - - tgcatta
- - - - - - - - - - - - - - - - - - - - - -ctcttgc