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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctccccataatcattaacctcaatttacatatcaaattggcagctgatccttctaatattagtatcatcttgaccccctcatttagacctagttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGG

Basic information

species Glycine max
transcript GLYMA11G37250.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 16
lower sequence: 13114.m00152 (Oryza sativa), 3'ss of exon 4
ctccccataatcattaacctcaatttacatatcaaa--ttggcagctgatccttctaatattagtatcatcttgaccccctcatttagacctagttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGG
     | || |   |   || || | | |    |||  |||  | |||||| | ||  | ||    |  |||   |    |  ||| |   |  |||| |||| ||| || || ||||| |||||  | ||||| || || || ||||||||||||||||||||||| || || |||||||   ||||||  ||||| ||||
--tttcctactggattttcttaactgaaagggaaaaacttgctaactgatcatacttctctttagtttttctattcataattttttggtttttttttttcagGTGGGAAAATTAGCTGACCTTGTTATTTGGAAACCTTCTTTCTTTGGAGCAAAACCAGAAATGGTTATAAAGGGTGGTGCTATTGCATGCGCTAATATGG

upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 16
lower sequence: AT1G67550.1 (Arabidopsis thaliana), 3'ss of exon 15
-----------ctccccataatcattaacctcaatttacatatcaa-attggcagctg-atccttctaatattagtatcatcttgaccccctcatttagaccta----gttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGG
            || ||| |    | |      | ||| | | |   |||  |  ||| | |    |||  | |||    | |||    | | |||   | ||     ||  |||||| |   ||| |||||||||||||  ||||| ||||| | || || |||||||||||||||||| | |||||||| ||  |  | ||||  ||||| ||||
gtatgctaatcttctccacacgtctcatatcttacttatacagctttattttcctctgtaactacttaacgtcagtgc--ttttgtttacttaattggaaactgcactgtgatgcagGTGAAGAAGCTGGCTGATCTTGTTATATGGCAGCCGGCTTTCTTCGGAGCAAAACCAGAAATGATAATCAAAGGAGGCAATATAGCATGGGCTAATATGG

upper sequence: GLYMA11G37250.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv01s0010g02760.t01 (Vitis vinifera), 3'ss of exon 15
--ctccccataatcattaacctcaatttacatatcaaattggcagctgatccttctaatattagta--tcatcttgaccccctcatttagacctagttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGG
   |     |  | |   |  |||   |     || |      || | |   | | || |||  |   || || |         || | |   |  ||   |||| ||| ||| |||||||||||||  | ||||| || || || ||||| |||||||||||||||||||| ||||||||||   ||||||  ||||||||||
gcttgtgtgtgtttacagagatcatactctggttccacccttgagtt-acattaccaaaattgtttactcgtccttgatgttgtatcttg---tgtttccacagGTGGGGAAGGTGGCTGATCTTGTTCTCTGGAATCCATCTTTCTTTGGGGCAAAACCAGAAATGGTGATAAAAGGTGGTGTAATTGCATGGGCTAACATGG

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|193646043|gb|FK588372.1|FK588372
EST:     TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAG                         GCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCA
genomic: TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAGgtataatgtt ... agttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCA
EST: gi|151405862|gb|EV275677.1|EV275677
EST:     TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAG                         GCGGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGC
genomic: TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAGgtataatgtt ... agttttgcagGCGGG-TAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGC
EST: gi|151402941|gb|EV272754.1|EV272754
EST:     TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAG                         GCGGGTAAGTTGGCTGATCTTGTATAATGGAAGCCGTCATTTTT-GGAGCA
genomic: TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAGgtataatgtt ... agttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCA
EST: gi|33388630|gb|CA851837.1|CA851837
EST:     TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAG                         GCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCA
genomic: TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAGgtataatgtt ... agttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCA
EST: gi|16277034|gb|BI942169.1|BI942169
EST:     TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAG                         GCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCA
genomic: TAAATCCAGCTATAGCGAATGGTTTGTCGCAATATGTTGGTTCAGTTGAGgtataatgtt ... agttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gatccttctaatattagtatcatcttgaccccctcatttagacctagttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGG
     ttctaatattagtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctccccataatcattaacctcaatttacatatcaaattggcagctgatccttctaatattagtatcatcttgaccccctcatttagacctagttttgcagGCGGGTAAGTTGGCTGATCTTGTATTATGGAAGCCGTCATTTTTTGGAGCAAAACCAGAAATGGTGATCAAAGGTGGTGAGGTTGCATATGCTAACATGG

ctcccca
- - - - - - - - acctcaa
- - - - - - - - - - - - - -catatca
- - - - - - - - - - - - - - - - - - - - cagctga
- - - - - - - - - - - - - - - - - - - - - - - - ccttcta