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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CACACAAAGTGTGAAGGATGGGGGGAAAGCTGTGATGATTGGACTGGCACAAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCCGAAAGgtgtgttctcttacttaactgttgtcaatgtgattgttaccggtactcccacatataaccactacctccattcagaatgaatttaaactgcttattatga...

Basic information

species Glycine max
transcript GLYMA05G33140.1
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G33140.1 (Glycine max), 5'ss of exon 7
lower sequence: AT5G63620.2 (Arabidopsis thaliana), 5'ss of exon 7
CACACAAAGTGTGAAGGATGGGGGGAAAGCTGTGATGATTGGACTGGCACAAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCCGAAAGgtgtgtt-ctcttacttaactgttgtcaatgtgattgttaccggtactcccacatataaccactacctccattcagaatgaatttaaactgcttattatga------------------------------
       |||||||| ||||| || ||||||||||||||||||||  |||||||||||||  | |||||  | || |||||||| ||||||||  ||||||| ||    |||||||       | ||    |  ||   |  |  | || |   ||     | |  ||      |  ||||  || ||   ||| || |                                
-------AGTGTGAAAGATGGTGGAAAAGCTGTGATGATTGGACTCTCACAAGCTGGTTCCGTTGGAGAAATTGACATAAATCGACTTGTTCGTAGAAAGGTTTGGGgttcttactctctctctctcggccttgttagaa--gaaagtctctggtactgagattgtcttttaagatcatgatattgaatctctttttgttctgtttttccaattttttgtgaagataaaag

upper sequence: GLYMA05G33140.1 (Glycine max), 5'ss of exon 7
lower sequence: AT5G63620.1 (Arabidopsis thaliana), 5'ss of exon 7
CACACAAAGTGTGAAGGATGGGGGGAAAGCTGTGATGATTGGACTGGCACAAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCCGAAAGgtgtgtt-ctcttacttaactgttgtcaatgtgattgttaccggtactcccacatataaccactacctccattcagaatgaatttaaactgcttattatga-----------------------
||||| ||||||||| ||||| || ||||||||||||||||||||  |||||||||||||  | |||||  | || |||||||| ||||||||  ||||||| ||    |||||||       | ||    |  ||   |  |  | || |   ||     | |  ||      |  ||||  || ||   ||| || |                         
CACACTAAGTGTGAAAGATGGTGGAAAAGCTGTGATGATTGGACTCTCACAAGCTGGTTCCGTTGGAGAAATTGACATAAATCGACTTGTTCGTAGAAAGgtttggggttcttactctctctctctcggccttgttagaa--gaaagtctctggtactgagattgtcttttaagatcatgatattgaatctctttttgttctgtttttccaattttttgtgaag
















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|254320053|gb|GR830969.1|GR830969
EST:     TATAAATCGGCTTGTTCGCCGAAAG                         ATACAAGTTATTGGCTCATATGGAGGCAGAGCGAGGCAAGATCTTCCTAAG
genomic: TATAAATCGGCTTGTTCGCCGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCATATGGAGGCAGAGCGAGGCAAGATCTTCCTAAG
EST: gi|254320052|gb|GR830968.1|GR830968
EST:     TATAAATCGGCTTGTTCGCCGAAAG                         ATACAAGTTATTGGCTCATATGGAGGCAGAGCGAGGCAAGATCTTCCTAAG
genomic: TATAAATCGGCTTGTTCGCCGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCATATGGAGGCAGAGCGAGGCAAGATCTTCCTAAG
EST: gi|193385062|gb|FK351516.1|FK351516
EST:     AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCCGAAAG                         ATACAAGTTATTGGCTCATATGGAGGCAGAG
genomic: AAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCCGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCATATGGAGGCAGAG
EST: gi|16348914|gb|BI974509.1|BI974509
EST:     GTTCGCCGAAAG                         ATACAAGTTATTGGCTCATATGGAGGCAGAGCGAGGCAAGATCTTCCTAAG
genomic: GTTCGCCGAAAGgtgtgttctc ... atttgagcagATACAAGTTATTGGCTCATATGGAGGCAGAGCGAGGCAAGATCTTCCTAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CACACAAAGTGTGAAGGATGGGGGGAAAGCTGTGATGATTGGACTGGCACAAGCTGGTTCTTTAGGAGAGGTGGATATAAATCGGCTTGTTCGCCGAAAGgtgtgttctcttacttaactgttgtcaatgtgattgttaccggtactcccacatataaccactacctccattcagaatgaatttaaactgcttattatga

- - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA