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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggttgtgactgtcgagtagctttattatctgaaattaggagtttgatattgacatattttatctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGATAGTTATGTGTTCAAAAGGGGATGCTGCCTCTGTATGCCCTAATGAATCT

Basic information

species Glycine max
transcript GLYMA09G38460.1
intron # 9
splice site 3'
intron type U2

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|298174671|gb|HO014702.1|HO014702
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|207813117|gb|GD783707.1|GD783707
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAG
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAG
EST: gi|207768257|gb|GD739941.1|GD739941
EST:     GCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|192325841|gb|FK018063.1|FK018063
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|58025101|gb|CX711842.1|CX711842
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
EST: gi|193468008|gb|FK434003.1|FK434003
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGGAACTTAATGCC
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCC
EST: gi|209696471|gb|BW664020.1|BW664020
EST:     GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAG                         CAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT
genomic: GATGAAAATCTCCCAATTGCTGTTGTAGCTACCCGTGATGCCTGCTTCAGgttggttgtg ... tctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagctttattatctgaaattaggagtttgatattgacatattttatctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGATAGTTATGTGTTCAAAAGGGGATGCTGCCTCTGTATGCCCTAATGAATCT
                              tattgac  putative branch site (score: 2)
                                        ttttatcttt  putative PPT
                         tttgatattgacatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggttgtgactgtcgagtagctttattatctgaaattaggagtttgatattgacatattttatctttgacagCAAACAGCAGTCTGTTATTCAGCAACTTAATGCCCGCAGAGGTCGTCTGATAGTTATGTGTTCAAAAGGGGATGCTGCCTCTGTATGCCCTAATGAATCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC