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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatatactgtgtaccttttatatttgttcaaacaactatatcaatctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA

Basic information

species Glycine max
transcript GLYMA18G47770.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os07g36190.1 (Oryza sativa), 3'ss of exon 4
gtatatactgtgtaccttttatatttgttcaaacaactatatcaatctactttgtcattgctgctttttgtttactttccccccactttgt--atgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA
|||| | |     |      |   | ||| |  | |    |  | |||  |  ||   ||||   |||   | |  ||     ||  || |   |  ||||| || |||||||| |||||||||||||| ||||||||||| || ||    ||||||||||| |||||||| || ||||||||  | ||||| || |||||
gtatgtgccaaaaaaa----aggctagttgaggcca----actattct--tccgtttctgctctgtttcaatgatgttagtaacatattatcattctccagGTGTTAGAAATGCTGCTCAGAGGAAGCTCTTGGATGAGCTGGGCATCCCAGCTGAAGATGTGCCAGTTGACCAATTCACCCCTCTTGGTCGGATGCTTTA

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G02780.1 (Arabidopsis thaliana), 3'ss of exon 4
----gtatatactgtgtaccttttatatttgttcaaacaactatatcaatctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA
    |||| |||||   |     | || |  |||     ||||| |  || ||        | |||  | |    |     |  || |||| |   | | |||| || || ||||| || || || |||||| | ||||||||||||||||| ||||||||||||||||| ||| ||||||| || ||||| || || || ||
gtgggtatctactggcaaaacaatttagtacttctttttactatct--atgtagaaaactgtagcttttctcaactag---tgacctcactgttactcatcagGTGTGAGGAATGCTGCACAAAGAAAGCTTCTCGATGAGCTTGGTATTGTAGCTGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGTATGCTGTA

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G16440.1 (Arabidopsis thaliana), 3'ss of exon 4
gtatatactgtgtac-cttttatatttgttcaaacaac-tatatcaatctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA
         || ||  || |||   ||  | ||||| | |  |||  ||  | ||   |  |||   |  || |   |        |  ||   | | |||| ||||||||||| || || ||||||||||| |||||||| |||||||| || |||||||||||||| ||| ||||||| || ||||| ||||| |||||
---------gtatatactcttaagctttatgaaacatcgtgaatctttcagcgttagta--gctatatactgatatatactattttatctttccttatcagGTGTAAGAAATGCCGCACAAAGGAAGCTTTTCGATGAGCTCGGTATTGTAGCAGAAGATGTACCAGTCGATGAGTTCACTCCCTTGGGACGCATGCTTTA

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g00600.t01 (Vitis vinifera), 3'ss of exon 4
gtatatactgtgtaccttttatatttgttcaaacaactatatcaatctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA
         || | || ||| | ||| |||        ||  || | | |||||||| |  ||  |||| ||   | |     || |   ||  |||||||||  | ||||| || || || ||||| |||||||| || || |||  ||||||||||| ||| |||||||||||||| ||| |||| ||||| |||||
---------gtattccattt-tctttcttcttttgga-atgccattatgctttgtcacta-tgacttttcttagttgtttgttcattcacta--accagGAGTGCGGAATGCTGCACAAAGAAAGCTGTTGGATGAACTCGGCATTCCTGCTGAAGATGCACCTGTTGATCAGTTCACTCCACTGGGCCGCATGCTTTA

upper sequence: GLYMA18G47770.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ31498 (Selaginella moellendorffii), 3'ss of exon 4
gtatatactgtgtaccttttatatttgttcaaacaactatatcaatctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA
                                  ||  |      | | ||| |  | ||||  |  |   | ||   | | |        |    ||||||||||||| || || || ||||||||||| |||||||| ||||| |  || |  ||    || || ||    |||||     |||| || || || ||
--------------------------------gtaaacaagcttgttttcttagctagtgct--tcctcactcacacacacacacacacacacccacagGAGTAAGAAACGCTGCGCAAAGGAAGCTTTTTGATGAGCTCGGTATCGCAGCAGCCGACTCCCCGGTGGACGCCTTCACTTTTCTGGGCCGGATCCTCTA

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|37997447|gb|CF809036.1|CF809036
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|26057349|gb|CA800263.1|CA800263
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|192320456|gb|FK012314.1|FK012314
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|18733450|gb|BM527614.1|BM527614
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|19934737|gb|BQ079767.1|BQ079767
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|15000069|gb|BI320883.1|BI320883
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|208176085|gb|GD974316.1|GD974316
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|19271109|gb|BM887365.1|BM887365
EST:     CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: CAGCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|254336566|gb|GR842745.1|GR842745
EST:     GCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: GCCATCCACTGTACCGTGAATCTGAGCTTATTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|208064082|gb|GD867024.1|GD867024
EST:     TTGATGAGAATGCCCTTG                         GAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
genomic: TTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG
EST: gi|207820807|gb|GD792574.1|GD792574
EST:     TTGATGAGAATGCCCTTG                         GNGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGC-TGGTATTGTTG
genomic: TTGATGAGAATGCCCTTGgtatatactg ... gtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA
                   ctttttgtttactttc  CT-rich tract
                    tttttgtttacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatatactgtgtaccttttatatttgttcaaacaactatatcaatctactttgtcattgctgctttttgtttactttccccccactttgtatgaccagGAGTAAGAAATGCAGCTCAGAGGAAGCTTTTGGATGAGCTTGGTATTGTTGCTGAAGATGTACCAGTTGATCAGTTCACCCCATTGGGTCGCATTCTTTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG