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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttgtttcccttaaaaaggttggtccctgatattttttttttcttaagtgagcatggggttttcattatcacttcgttttcttcccaactttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTAGCACAAGGTGCTAGAAATGCAGCAGATATAGCAGATTCTACACTTAATA

Basic information

species Glycine max
transcript GLYMA06G09240.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G09240.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv04s0008g00200.t01 (Vitis vinifera), 3'ss of exon 14
--ttgtttgtttcccttaaaaaggttggtccctgatattttttttt--tcttaagtgagcatggggttttcattatcacttcgttttcttcccaactttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTAGCACAAGGTGCTAGAAATGCAGCAGATATAGCAGATTCTACACTTAATA
  ||||||  |       |||   |   |      || |  | ||   | ||   |||  |||| ||    || || | || | |||  |    ||||| |||||||||||| |||||||| ||||| ||||||| |||||| ||| |  | || ||| | ||||| | ||| || ||||||||||| ||| |||| || ||||
gattgttttctgtatcagaaagtatatattttctttactgatgttcaatttttgctgattatggtgtcccaatcatgaatttggttttct----acttttgcagGTTCGCTACGAGGAAATTATGTCTGATTCAGCTTATTTGGATAGGCTCTTGGCAGAGGGTGCCACAAAAGCTGCAGATATAGCTGATGCTACTCTCAATA
















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|22929614|gb|BU546753.1|BU546753
EST:     TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAG                         GTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA
genomic: TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAGgtttcaccta ... actttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA
EST: gi|15203981|gb|BI426758.1|BI426758
EST:     TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAG                         GTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA
genomic: TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAGgtttcaccta ... actttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA
EST: gi|15662082|gb|BI699453.1|BI699453
EST:     TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAG                         GTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA
genomic: TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAGgtttcaccta ... actttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA
EST: gi|8404302|gb|BE059936.1|BE059936
EST:     TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAG                         GTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA
genomic: TCAAACCTCTTTTAACAGATGCCTTGATTGATCATTTGCATCCCATTCAGgtttcaccta ... actttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttaagtgagcatggggttttcattatcacttcgttttcttcccaactttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTAGCACAAGGTGCTAGAAATGCAGCAGATATAGCAGATTCTACACTTAATA
                             cttcgttttcttccca  CT-rich tract
                 ttttcattat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttgtttcccttaaaaaggttggtccctgatattttttttttcttaagtgagcatggggttttcattatcacttcgttttcttcccaactttggcagGTTCGCTATGAGGAAATCATGTCCGATTCAGGTTATTTAGATGGAGTTTTAGCACAAGGTGCTAGAAATGCAGCAGATATAGCAGATTCTACACTTAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - gtttccc
- - - - - - - - - - - - - tccctga
- - - - - - - - - - - - - - - - - - - - - - - - - - - gcatggg