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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgttgctctttagatttatgttaaattgatttcattttgtattctaattttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG

Basic information

species Glycine max
transcript GLYMA16G01230.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g42380.1 (Oryza sativa), 3'ss of exon 4
---------------gtaagtgttgctctttagatttatgttaaattgatttcattttgtattctaa------ttttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
                | | |  ||||  || | |  |  |||| |   |||  |||| |   | ||        || |   ||     | ||| |||||||||| ||||| |||||||||||||||||| ||||| ||||| ||||| ||  |||
gtaagagaaaagctattcatttctgctagtttgttgaagcttaattatgtttttttttctccccaaaaacactcattgaagaaaaatgatacagTTTTGGGCAGCTTATCAGAGTTAATTGGGCATATGCTAGTGGGCAGAGGGAGGACACAACAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g40510.1 (Oryza sativa), 3'ss of exon 4
----------------------------gtaagtgttgctctttagatttatgttaaattgatttcattttgtattctaattttaattcaatgctttgc-agATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
                             ||  | |   |  | | ||||   ||    |  |  ||||||  |   |  | |||      | | || | || ||||| ||||| || ||||| |||||||||||||| |||  ||| ||||||||||| ||||
gtaagtatttcaatactatagtattataatatatataaattctaatattttgcttttcctcttaacattttccaacattttcttatgatcctacattaccagGTTTGGCCAGCCAATAAAAGTCAATTGGGCATATGCAAGTACTCAAAGAGAGGATACATCAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G17370.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------gtaagtgttgctctttagat-ttatgttaaattgatttcattttgtattctaatttt---aattcaatgctt---------tgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
               | | | ||   |||| |   || |   |     |    | | ||| ||| || |||   | | || || ||         ||||| |||||||| |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||| 
gtaagttaatggacatgattattagcctttgggcattttagcatgaacaagatactctgttttccaagttttggattacattgtttactctaatgtgcagGTTTGGGCAACCTATCAAGGTTAACTGGGCTTATGCGAGTGGCCAGAGGGAGGATACATCAA

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G54080.2 (Arabidopsis thaliana), 3'ss of exon 4
-------gtaagtgttgctctttagatttatgttaaattgatttcattttgtattct----aattttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
          |   ||| |  ||     | || | | |  ||||  |  ||| ||||     ||| ||||       ||  ||||||||| |||||||| |||||||||||||| ||||| | |||||| || || ||||| ||| 
gtaagaatctaacattgatacttcatgctttgattagtcaatttattcatgtgttctcttagattataatattggatttcacagATTTGGACAGCCTATGAAAGTTAATTGGGCGTATGCAACTGGTCAAAGGGAAGATACATCAA

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G14100.1 (Arabidopsis thaliana), 3'ss of exon 4
------------gtaagtgttgctctttagatttatgttaaattgatttcat-tttgtattctaattttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
             |   |  |   |||    |     |   || | |   ||  || | ||    || ||||       ||| ||| ||||| |||||||||||||| |||||||| ||||| | ||||||||| || ||||| ||| 
gtaaggaacaattttcatagtttccttcctctcctcttcttatcgttcgaatgcttttgtttaggttataatcgtcgagtttacagGTTTGGACAGCCTATCAAAGTCAATTGGGCGTATGCCACTGGTCAGAGGGAAGATACATCAA

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv09s0002g00880.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtgttgctctttag----atttatgttaaattgatttcattttgtattctaattttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
|||||     | ||| |     |||||||||| ||   ||    ||||| ||||  |  | |||   |  ||||||| ||||||||||||||||||||||||||||||||||| |||||||| || ||||| || ||||
gtaagaagaacccttgatttttatttatgttacat--gttgggatttgt-ttctgttgctcattttgtaatttgcagGTTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCTAGTGGTCAAAGGGAGGACACATCAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S84_50V6.2 (Physcomitrella patens), 3'ss of exon 5
----------------------gtaagtgttgctctttagatttatgttaaattgatt-tcattttgtattctaattttaatt----caatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
                       ||| | |   |    |          |||| |||  | ||||  | |||| || |   |       ||||| || |||||||| ||||||||||||||||||||||||||||| || || ||||||||||||||  |||
cgtcttcactttttgtgctttcctaattttccttacgaatgcaaggaccaaatagatagtaatttctttttctgatctgcgtggtgatgatgctgtgtagATTTGGACAGCCTATCAAAGTTAATTGGGCATATGCAAGCGGGCAGAGAGAGGATACTACAG

upper sequence: GLYMA16G01230.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S84_51V6.1 (Physcomitrella patens), 3'ss of exon 4
------------------------gtaagtgttgctctttagatttatgttaaatt-gatttcattttgtattctaattttaattcaa--tgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
                          ||  |  |   |    |||  | |  | || ||  |    | | ||||| |  |    | |   || ||||||| ||||||||  |||||||||| ||||||||||||||||| || || |||||||||||  |||
tggtcgcaaatagttttaaaacgataaaacgacgaaatccgaattcttatggattttgaaattggctggcattctcaaatactctgaggctgatttgcagGTTTGGGCAATCTATCAAAGTAAATTGGGCATATGCGAGCGGACAAAGAGAGGATACAACAG

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|5606316|gb|AI900414.1|AI900414
EST:     GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT                         ATTTGTGCAGNCTATCAAAGTTAATT
genomic: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttg ... tgctttgcagATTTGGGCAGCCTATCAAAGTTAATT
EST: gi|209725663|gb|BW663152.1|BW663152
EST:     GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT                         ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGA
genomic: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttg ... tgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGA
EST: gi|4313794|gb|AI460913.1|AI460913
EST:     GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT                         ATTTGGGCAGCCTATCAAAGT
genomic: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttg ... tgctttgcagATTTGGGCAGCCTATCAAAGT
EST: gi|298165726|gb|HO008697.1|HO008697
EST:     GATCGCAGATCTGCTGCTCTTGCCATATTATCTCCCAATGGAAGGTATCT                         ATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGA
genomic: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttg ... tgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGA
EST: gi|5058332|gb|AI736808.1|AI736808
EST:     GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCT                         ATTTGGGCAGCCTATCAAAGTTAATT
genomic: GATCGCAGATCTGCTGCTCTTGCCATATTATCTCTCAATGGAAGGCATCTgtaagtgttg ... tgctttgcagATTTGGGCAGCCTATCAAAGTTAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttatgttaaattgatttcattttgtattctaattttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG
       ttaaattgatttcatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgttgctctttagatttatgttaaattgatttcattttgtattctaattttaattcaatgctttgcagATTTGGGCAGCCTATCAAAGTTAATTGGGCATATGCGAGTGGTCAGAGAGAGGATACGTCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT