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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGGAAGATCGCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttgtttttgtttttgtcttcctatgcatacatatatggatggcatgatttctgattttgatgtgttctgtggtgaatggtgattttgttgtag

Basic information

species Glycine max
transcript GLYMA02G46230.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G46230.1 (Glycine max), 5'ss of exon 3
lower sequence: AT4G26850.1 (Arabidopsis thaliana), 5'ss of exon 3
TGGGAAGATCGCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgt--ctgttttgttt---ttgttt--ttgtcttcctatgcatacatatatggatggcatgatttctgattttgatgtgttctgtggtgaatggtgattttgttgtag------
||||| ||| |  | || ||||||||||||||||||||||| || ||||| |||||||| ||   ||| ||  ||   ||||||     |||   ||||      | | ||      | || | |    | || | |    |||  | ||   || || | |||  |      
TGGGAGGATAGGTTCCAAAGAGGACTTTTTCGCTATGATGTCACTGCCTGCGAAACCAAAgtaattgtctttcttaccttgtttgacaatctagttatgttgggttgtttgttgctgaggaatccgagatatgttttacattgttcttaagattgtttctcttgatgttatag

upper sequence: GLYMA02G46230.1 (Glycine max), 5'ss of exon 3
lower sequence: AT5G55120.1 (Arabidopsis thaliana), 5'ss of exon 3
TGGGAAGATCGCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgt-ctgttttgtttttgtttttgtcttcctatgcatacatatatggatggcatgatttctgattttgatgtgttctgtggtgaatggtgattttgttgtag---
|||||||||||  | || ||||| ||||||||||||||||| |||||||| |||||||||||  | || | | |||| ||||   ||  |     ||| | || |      ||| | | |||| || |  ||  |||  |   ||   | ||  | |       
TGGGAAGATCGTTTCCAAAGAGGTCTTTTTCGCTATGATGTCACCGCCTGCGAAACCAAGgtattattgtctctttgatttttggttaattgatttactttta-gagccaaatg-tgtttgatgtttacttgacctgaagc--atcaagtttcagctcacattg
















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|12691114|gb|BG157450.1|BG157450
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
EST: gi|11413167|gb|BF425178.1|BF425178
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
EST: gi|7326625|gb|AW620423.1|AW620423
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
EST: gi|207808432|gb|GD777647.1|GD777647
EST:     GCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
genomic: GCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
EST: gi|27445855|gb|CA952978.1|CA952978
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAG
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAG
EST: gi|193526304|gb|FK481604.1|FK481604
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAG
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAG
EST: gi|22541283|gb|BU091126.1|BU091126
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
EST: gi|14205548|gb|BG839226.1|BG839226
EST:     GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCMTGTGAAACCAAG                         GTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC
genomic: GCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttg ... tttgttgtagGTGATTCCTGGTGAATATGGTTTCGTTGCCCAGCTTAACGAGGGTCGTCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGGAAGATCGCATGCAGAGAGGACTTTTTCGCTATGATGTTACCGCCTGTGAAACCAAGgtctgttttgtttttgtttttgtcttcctatgcatacatatatggatggcatgatttctgattttgatgtgttctgtggtgaatggtgattttgttgtag

- - - - - - - -  GAGAGG
- - - - - - - - - AGAGGA