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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTAATTGGAAACGTGAGCATACAATGGAAGACGTTTTGATTCAATTGAAGAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctatcttatttttatagttgctatttgtttatatatacattttatcaatttctatatggttaaaatgtctttcataattgctagtagtttctat...

Basic information

species Glycine max
transcript GLYMA09G22600.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 4
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 5'ss of exon 4
GCTAATTGGAAACGTGAGCATACAATGGAAGACGTTTTGATTCAATTGAAGAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctatcttattttta-tagttgctatttgtttatatatacattttatcaatttctatatggttaaaatgtctttcataattgctagtagtttctat--
|||| |||| |  | |||||||||||||| ||| | |||| ||||||||||| ||||||||||||||| || ||| | |||||  ||||||||||||||||| |||  || || ||| |  |  |||  |    |   | | | | || ||||   ||| | || |||||||      | | ||  |    | || | | |  
GCTACTTGGCAGAGGGAGCATACAATGGAGGACATATTGACTCAATTGAAGAAAGAAATGATGTCTCCCCAGAATCGAAAGCTGGCTCAGCCTCCTGAAGgtttgttaattttgtttctggtgattgacagaaata-gtgttttctttctatct-cttcaagattgttaaaaaaaaaat-aaaagggaagattgtctttgtag
















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|298168826|gb|HO009756.1|HO009756
EST:     GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAG                         GCAATGAAGAAGCC
genomic: GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctat ... tatgacatagGCAATGAAGAAGCC
EST: gi|6071962|gb|AW101349.1|AW101349
EST:     GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAG                         GCAATGAAGAAGCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGTTGTA
genomic: GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctat ... tatgacatagGCAATGAAGAAGCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGTTGTA
EST: gi|33387487|gb|CA850694.1|CA850694
EST:     GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAG                         GCAATGAAGAAGCCAGGGTTGATCAAGAGGGCCTGGTGGTGAGATGTTGTA
genomic: GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctat ... tatgacatagGCAATGAAGAAGCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGTTGTA
EST: gi|21285722|gb|BQ473593.1|BQ473593
EST:     GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAG                         GCAATGAAGAAGCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGGTGTA
genomic: GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctat ... tatgacatagGCAATGAAGAAGCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGTTGTA
EST: gi|22522487|gb|BU081298.1|BU081298
EST:     GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAG                         GCAATGAAGAAGCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGTTGTA
genomic: GAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctat ... tatgacatagGCAATGAAGAAGCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGTTGTA
EST: gi|19269626|gb|BM885882.1|BM885882
EST:     AAGAGAA-TGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAG                         GCAATGAAGAAAGC-AGGGTTGATCAAAAGGGCCTGGTGGTGAGATGT
genomic: A-GAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctat ... tatgacatagGCAATGAAGAA-GCCAGGGTTGATCAAAAGGGCCTGGTGGTGAGATGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTAATTGGAAACGTGAGCATACAATGGAAGACGTTTTGATTCAATTGAAGAGAGAAATGATGTCTCCTCAAAATAGGAAGCTAACTCAGCCTCCTGAAGgtgtgtctatcttatttttatagttgctatttgtttatatatacattttatcaatttctatatggttaaaatgtctttcataattgctagtagtttctat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG