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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatccaaaatgggcttctttgtactgctttcctctttagttatgctttcacgaagatagttttaaattttattttttgaattttttatattttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTTTTATTGATCCAAGTACAGAGAAAATCAGGACAATACCATTAGAAATTAC

Basic information

species Glycine max
transcript GLYMA19G01260.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G01260.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os08g29370.1 (Oryza sativa), 3'ss of exon 4
atatccaaaatgggcttctttgtactgctttcctctttag--ttatgctttcacgaagatagttttaaattttattttttgaattttttata---ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTTTTATTGATCCAAGTACAGAGAAAATCAGGACAATACCATTAGAAATTAC
       ||   | ||   | ||  | || |  | |||||  ||  |   |||  |   || || |  | |    ||||   |  | ||||    | || |||||| ||||| |||||||| |||||||| |||||||| || || |||||||| ||||||||||| ||||| |  ||| |  | ||||||||  | ||  | | 
-----tgaagaagcctctctagttgttctctgttatttaggattgagaagtcagaaccttaattatctagtgagcttttgttaactattatcggttcttttgcagCTGATGGTTTTGTTGTTCAAACTGGCGATCCTGAGGGACCAGCTGAGGGATTTATTGATCCCAGTACTGGTAAAGTTCGTACAATACCTCTTGAGTTAAT

upper sequence: GLYMA19G01260.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv14s0066g01410.t01 (Vitis vinifera), 3'ss of exon 4
atatccaaaatgggcttctttgtactgctttcctctttagttatgctttcacgaagatagttttaaattttattttt--tgaattt----tttatattttgt-gcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTTTTATTGATCCAAGTACAGAGAAAATCAGGACAATACCATTAGAAATTAC
      |  |  | || | |  | ||   ||  |  ||   |||   |  || | | ||  || | | |||  |||   | ||  |    ||||  |||||| ||||| ||||| |||||||| |||||||| |||||||| |||||||| ||||| |||||||||||||||||||| ||   | ||||| ||||| | ||||| | 
------actactgcctccatcatgcttagttgataatttcatat-tgtatacaatgctaagttgatagttttctttcgataaaactcagatttactttttgttgcagCTGATGGATTTGTTGTTCAAACTGGAGATCCTGAGGGTCCTGCAGAGGGCTTTATTGATCCAAGTACAGAAAAGCCCCGGACAGTACCACTTGAAATCAT
















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|15589721|gb|BI674337.1|BI674337
EST:     TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAG                         CGGATGGGTTTGTTGTCCAAACTGGTGTTCCTGAAGGTCCTGCTGAGGGTT
genomic: TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAGgtaataaatc ... ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT
EST: gi|13480110|gb|BG509453.1|BG509453
EST:     TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAG                         CGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT
genomic: TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAGgtaataaatc ... ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT
EST: gi|20208026|gb|BQ134115.1|BQ134115
EST:     TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAG                         CGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT
genomic: TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAGgtaataaatc ... ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT
EST: gi|27424039|gb|CA935559.1|CA935559
EST:     TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAG                         CGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT
genomic: TGTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAGgtaataaatc ... ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT
EST: gi|20812710|gb|BQ297188.1|BQ297188
EST:     GTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAG                         CGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGACCTGCTGAGGGTT
genomic: GTTGATTTGGTAGAAAGGCACTTCTATGATGGCATGGAAATCCAAAGAGgtaataaatc ... ttttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttcacgaagatagttttaaattttattttttgaattttttatattttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTTTTATTGATCCAAGTACAGAGAAAATCAGGACAATACCATTAGAAATTAC
           atagttttaaatttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatccaaaatgggcttctttgtactgctttcctctttagttatgctttcacgaagatagttttaaattttattttttgaattttttatattttgtgcagCGGATGGGTTTGTTGTCCAAACTGGTGATCCTGAAGGTCCTGCTGAGGGTTTTATTGATCCAAGTACAGAGAAAATCAGGACAATACCATTAGAAATTAC

- atccaaa
- - - - - - -gcttctt
- - - - - - - - - - - - -tgctttc