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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGGGACAGATTGTTGAAGCAGGGAGGGAAATCTCCAGTCTTTCTGAAAGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgattttctaaatttctgttaactttaggtttcattttccattgttttgtctcatttccatattcccttttcag

Basic information

species Glycine max
transcript GLYMA02G08440.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA02G08440.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv18s0001g01940.t01 (Vitis vinifera), 5'ss of exon 4
TGGTGGGACAGATTGTTGAAGCAGGGAGGGAAATCTCCAGTCTTTCTGAAAGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGC---AAGATAA---TAAACgttagtgattttctaaatttctgttaactt--taggtttcattttccattgttt--tgtctcatttccatattcccttttcag-----------------------
         |||||||| ||||||| ||||||| | || || |||||||||||||||||||| ||||||||||||||||||||||| |   |||||||   |||||||  || || || | |||  || ||||  |  |   || |  |||||||| |||  ||||| |    | | ||  |||  |                         
------AGTAGATTGTTAAAGCAGGAAGGGAAACCACCTGTGTTTCTGAAAGTTGATTGGGACAAATGGGTTGATGAAGATGAGGAACCGGAAGATAAAGATAAACgtgtgtcatgttttcaatccctcttaaaatagtcaattaccgtttccattttttactgtctgaaaaacttgttggcttgcctttgacatgatattttggtttacag
















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|7042420|gb|AW472314.1|AW472314
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTGTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|254343607|gb|GR857363.1|GR857363
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|8402677|gb|BE058311.1|BE058311
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|298162968|gb|HO011701.1|HO011701
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|192302805|gb|FG998487.1|FG998487
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGANNNNNNN
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|9985951|gb|BE659957.1|BE659957
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|193599852|gb|FK551591.1|FK551591
EST:     GATGAAGATGAGGAGCAAGATAATAAAC                         CTGGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: GATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCT-GCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|298172800|gb|HO020354.1|HO020354
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|192302804|gb|FG998486.1|FG998486
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
EST: gi|24205344|gb|BU964597.1|BU964597
EST:     AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAAC                         CTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT
genomic: AGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgatt ... cccttttcagCTGCAGCATCTGATATGGACTTTGGTGACATTGATTTTTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGGGACAGATTGTTGAAGCAGGGAGGGAAATCTCCAGTCTTTCTGAAAGTTGATTGGGATAAATGGGTTGATGAAGATGAGGAGCAAGATAATAAACgttagtgattttctaaatttctgttaactttaggtttcattttccattgttttgtctcatttccatattcccttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA