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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggggaagcacttgtttttaatattctcaaagaggttaatatgatctcataatttttttccttgcaagatatgaattatttccccctggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTGTCCTGATCCTAGAATTGTTACAGTTTGTCTGGAAGGCCTTGAAAACATC

Basic information

species Glycine max
transcript GLYMA20G38320.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G38320.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 9
----------gtatggggaagcacttgtttttaatattctcaaagaggt-taatatgatctcataatttttttccttgcaagatat---gaattatttccccctggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTGTCCTGATCCTAGAATTGTTACAGTTTGTCTGGAAGGCCTTGAAAACATC
           |     |  |||||   ||||    |   ||     ||  |||   | || ||   | |   | ||| | |  ||   ||| |  |      |  |    |||| | | ||     | || || || ||||| |||||||| |||||  |||| |||||||| |||||||| |||||||||||||| || || || || || 
gtatactaccttgacttgctgcactgccttttggcttgtgcagttgtgtgcaatgcaa-cttatgtatgtcacctttgaacggaatttagaactcatgttttgtcttgcatagGTACTTGGTGTCTGAGGGCTGCATCAAGCCATTGTGTGACCTTCTTGTCTGCCCTGATCCGAGAATTGTAACAGTTTGTCTGGAGGGTCTGGAGAATATT

upper sequence: GLYMA20G38320.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 8
-----gtatggggaagcact----tgtttttaatattctcaaagaggttaatatg-atctcataatttttt---tccttgcaagatatgaa--ttatttccccctggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTGTCCTGATCCTAGAATTGTTACAGTTTGTCTGGAAGGCCTTGAAAACATC
      |||   ||   |||    || ||||    || |  |   |  |   ||| | || ||   | | |   | |   ||  || |  |  | || |  |          |||| | | ||     | || || ||   |||  |||| || |||||  | || |||||||| |||||||| |||||||||||||| || ||||| || || 
gtatactatcttgacttactgcactgctttttgccttgtgcagttgtgtgcaatgcaacttatgtatgtctgagttcgaacataatttagaactcatgttgcgtcttgcaatagGTACTTGGTGTCTGAGGGCTGCATCGTGCCGCTGTGCGACCTTCTTGTTTGCCCTGATCCGAGAATTGTAACAGTTTGTCTGGAGGGTCTTGAGAATATT

upper sequence: GLYMA20G38320.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 9
gtatggggaagcacttgtttttaatattctcaaagaggttaatatgatctcataatttttttccttgcaagatatgaattatttccccctggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTGTCCTGATCCTAGAATTGTTACAGTTTGTCTGGAAGGCCTTGAAAACATC
|||||     | |      |||  | ||||||      |||  |   |       | ||| | | |||| | | |  ||| | |   |   | |  ||||| |||||| || ||||  |  || ||||||||||||||||||||  |||| ||||||||  | ||||| ||||||||| | ||||| ||||| ||||||
gtatgatcttg-atagaaatttcttgttctcatgtc--ttagcagtcttgttctgtgtttctgcatgcatgttttttattctctttgct--gatgacagGTACCTAGTTAGTCAAGCATCCATCAAGCCCTTGTGTGATCTTCTGGTCTGCCCTGATCCACGGATTGTCACAGTTTGTTTAGAAGGGCTTGAGAACATC

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|254331218|gb|GR845797.1|GR845797
EST:     GCTTGGGCTATCTCAAATGCTACATCCGGTGGTTCTCATGAACAAATCAA                         GTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG
genomic: GCTTGGGCTATCTCAAATGCTACATCCGGTGGTTCTCATGAACAAATCAAgtatggggaa ... tggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG
EST: gi|207802396|gb|GD775628.1|GD775628
EST:     TTGGGCTATCTCAAATGCTACATCCGGTGGTTCTCATGAACAAATCAA                         GTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG
genomic: TTGGGCTATCTCAAATGCTACATCCGGTGGTTCTCATGAACAAATCAAgtatggggaa ... tggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG
EST: gi|22525688|gb|BU084499.1|BU084499
EST:     GCTTGGGCTATCTCAAATGCTACATCCGGTGGTTCTCATGAACAAATCAA                         GTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG
genomic: GCTTGGGCTATCTCAAATGCTACATCCGGTGGTTCTCATGAACAAATCAAgtatggggaa ... tggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG
EST: gi|23053056|gb|BU577547.1|BU577547
EST:     TTCTCATGAACAAATCAA                         GTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG
genomic: TTCTCATGAACAAATCAAgtatggggaa ... tggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatctcataatttttttccttgcaagatatgaattatttccccctggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTGTCCTGATCCTAGAATTGTTACAGTTTGTCTGGAAGGCCTTGAAAACATC
                                     tttccccctggttt  CT-rich tract
                        aagatatgaattattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggggaagcacttgtttttaatattctcaaagaggttaatatgatctcataatttttttccttgcaagatatgaattatttccccctggtttgcagGTTCCTAGTAAGCCAAGGGTGTATTAAGCCCTTGTGTGATCTTCTCATCTGTCCTGATCCTAGAATTGTTACAGTTTGTCTGGAAGGCCTTGAAAACATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG