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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtccattagacatttctttggtgtatcttatttcatttctctcatttatatgatctttttattttttttttattttttttttttttgtatttcactcactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAG

Basic information

species Glycine max
transcript GLYMA05G14170.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 4
gttagtccattagacatttctttggtgtatcttatttcatttctctcatttatatgatctttttattttttttttattttttttttttttgtatttcactcactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAG
                        ||  |  || || | ||   |  |||   ||  | | | ||        || || ||| |   ||  ||||    |  ||  ||||||||| |||||||||||||| |||||||||||||| || |  ||||| || || || ||||| || ||||  |||
------------------------gttcagtttcttgccttatccaaattagaat--tttatgtaccaaaagattgttctttataccttgctattct--ttgctgcgcagAGATTATGGTTTAAGACAAACCTGAAGCTTTGCAAAATTTGGTTTGACATGGGGGAGTATGGCCGGATGAGCAAG

upper sequence: GLYMA05G14170.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 4
gttagtccattagacatttctttggtgtatcttatttcatttctct-catttatatgatctttttattttttttttattttttttttttttgtatttcactcactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAG
         |||    ||| |||  ||| |   | || ||| |||| || || | |||   | ||| ||||    ||| ||  | | ||               |  ||||||||||||||||||||||||||| |||||||||||||| |  || || || |||||||||||||| |||| ||||
--------gttacgggttttttt--tgtcttaaactttattgctcttcacttgt-tgaggatgttagttttaaaatatattactctctt-------------gatgggcagAGATTGTGGTTTAAGACAAATCTTAAGCTTTGCAAGATTTGGTTCGACATGGGTGAATATGGGCGAATGAGTAAG
















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|8283183|gb|BE020744.1|BE020744
EST:     AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAG                         AGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATT
genomic: AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAGgttagtccat ... cactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATT
EST: gi|17518821|gb|BM187863.1|BM187863
EST:     AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAG                         AGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATT
genomic: AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAGgttagtccat ... cactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATT
EST: gi|298194816|gb|HO043288.1|HO043288
EST:     AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAG                         AGATTGTGGTTTAAGACAAATCTGAAGCTTTGCA-GATATATTT-GATATT
genomic: AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAGgttagtccat ... cactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATT
EST: gi|18690841|gb|BM519689.1|BM519689
EST:     AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAG                         AGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATT
genomic: AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAGgttagtccat ... cactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATT
EST: gi|298169723|gb|HO021083.1|HO021083
EST:     AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAG                         AGATTGTGGTTTAAGAC
genomic: AGGAATTCTACCAGACTACTCTGAGGTCCCTTGAAGATGCAAAGAACGAGgttagtccat ... cactatgcagAGATTGTGGTTTAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatctttttattttttttttattttttttttttttgtatttcactcactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAG
                                         cactcac  putative branch site (score: 2)
       ttattttttttttatt  CT-rich tract
     ttttatttttttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtccattagacatttctttggtgtatcttatttcatttctctcatttatatgatctttttattttttttttattttttttttttttgtatttcactcactatgcagAGATTGTGGTTTAAGACAAATCTGAAGCTTTGCAAGATATATTTTGATATTGGTGAATATGGGCGTATGAATAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA