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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtatttcttttctaatatctagttatacctttaacagtgtcaattgatattttctttcattctcttgattatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAATAATGGTTCCTTATAACAACAAGAAGTATTACATTGACATAGTTGAAACT

Basic information

species Glycine max
transcript GLYMA15G04140.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04140.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G29070.2 (Arabidopsis thaliana), 3'ss of exon 6
gttagtatttctttt-ctaatatctagttatacctttaacagtgtcaattgatattttctttcattctcttgattatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAATAATGGTTCCTTATAACAACAAGAAGTATTACATTGACATAGTTGAAACT
||| ||| || |    || |    |  |  | |  || |   ||    |  | | | | |||| |    ||  |  |||||||||| |||||||| |||||||| ||||| || ||||| || ||||| ||||| |||||||| |||||||||||| | ||||||||  |  | |||||  | 
gtttgtagttttgaaactgaatagttttcgttctattgaatatggttttgaagaatgtgtttcttatcattcctcttttgcagCTTGGAGACTACGCTTAGGAGTTACTCTTGCTTAACCACGGGTGATACAATTATGGTTCCGTATAACAACAAGCAATATTACATCAATGTGGTTGAGGCA

upper sequence: GLYMA15G04140.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv06s0004g05010.t01 (Vitis vinifera), 3'ss of exon 3
--gttagtatttcttttctaatatctagttatacctttaacagtgtcaattgatattttctttcattctcttgattatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAATAATGGTTCCTTATAACAACAAGAAGTATTACATTGACATAGTTGAAACT-------
   || |  |||||||    ||    ||    | ||| |    | ||  || || |||  |||  ||||     ||| |||| | || ||||||| | | ||||||| ||| |||||||| ||||||||||| ||| || ||  ||||| ||| ||||||| ||||||||| ||||| || ||        
gttttggagtttctttcgccattgtcaga-gcagcttgatgtttttctttttatgtttcttttacttcttcatgttacttgctggttggagACTAAATTGAGGAGCTTCTCTTGTTTAACTACTGGTGACACCATAGTGATTGATTATAGCAATAAGAAGTTTTACATTGATATAGTAGACACCAAACCCT
















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|209707768|gb|BW683660.1|BW683660
EST:     CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCAT                         CTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT
genomic: CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCATgttagtattt ... ttatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT
EST: gi|298175906|gb|HO015311.1|HO015311
EST:     CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCAT                         CTTAGAGACTACACTTAGGAGCTACTCA
genomic: CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCATgttagtattt ... ttatttgcagCTTAGAGACTACACTTAGGAGCTACTCA
EST: gi|37993996|gb|CF805742.1|CF805742
EST:     CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCAT                         CTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT
genomic: CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCATgttagtattt ... ttatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT
EST: gi|120533678|gb|EH261811.1|EH261811
EST:     CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCAT                         CTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT
genomic: CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCATgttagtattt ... ttatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT
EST: gi|15664016|gb|BI701387.1|BI701387
EST:     CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCAT                         CTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT
genomic: CTGCAGCCTCACACAAAGGATTTTTTGGATATCTCCAATCCAAAAGCCATgttagtattt ... ttatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatacctttaacagtgtcaattgatattttctttcattctcttgattatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAATAATGGTTCCTTATAACAACAAGAAGTATTACATTGACATAGTTGAAACT
                          ttttctttcattctct  CT-rich tract
                  aattgatattttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtatttcttttctaatatctagttatacctttaacagtgtcaattgatattttctttcattctcttgattatttgcagCTTAGAGACTACACTTAGGAGCTACTCATGTTTAACAACTGGTGACACAATAATGGTTCCTTATAACAACAAGAAGTATTACATTGACATAGTTGAAACT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT