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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taattttctaacttgaaactaaacatgcacacacctttatttgatttatggaaaagaagaataaaataaaatattgggtattggaatgtttgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGACAGTCATGGGTCCAATTCCGGGCGTTAAATATGATGAGAGGAGACAACGA

Basic information

species Glycine max
transcript GLYMA15G02280.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G02280.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g03450.t01 (Vitis vinifera), 3'ss of exon 2
taattttctaacttgaaactaaacatgcacacacctttatttgatttatggaaaagaagaataaaataaaatattgggtattggaatgtttgcat-tgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGACAGTCATGGGTCCAATTCCGGGCGTTAAATATGATGAGAGGAGACAACGA
    ||||| | |  |  ||  |  |  |   | || ||    || | |  |  |     ||    |    | ||  ||  || | | | ||  | |||||||| ||| | ||||| ||||||||||| ||| |||| ||||| ||||||||  | ||||||||||| || |  || ||||||||||||   |||||| | 
---gtttctgattccacccttcaagtttagcaatctgta---aatatttaaatcacgccgattgt-tgctgtgttttgt-ctgaattctgtgtctctgcagGGCTGCTCAGCTGGGAATGAAGTTGGAGTGGATGGAGGATGGTGTGAAGACGATAATGGGTCCAATCCCAGCTGTCAAATATGATGAGTCAAGACAAAGG
















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|22929485|gb|BU546624.1|BU546624
EST:     GGCTGGAAATCTANNNTCTTGACCACTGACAAGACCCTCGCTCAACAAAG                         GGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
genomic: GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAGgtttctctac ... tgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
EST: gi|7925929|gb|AW831955.1|AW831955
EST:     GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAG                         GGCTGCTAAACTGGGTATGAAGTTGGAATGGTTGTAAGATGG
genomic: GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAGgtttctctac ... tgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGG
EST: gi|6848665|gb|AW350955.1|AW350955
EST:     CTTGACCANNGACAAGACNNNCGCTCAACAAAG                         GGCGGNNAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
genomic: CTTGACCACTGACAAGACCCTCGCTCAACAAAGgtttctctac ... tgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
EST: gi|31307898|gb|CD393101.1|CD393101
EST:     GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAG                         GGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
genomic: GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAGgtttctctac ... tgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
EST: gi|13479384|gb|BG508727.1|BG508727
EST:     GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAG                         GGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGACTGGGGTGAAGA
genomic: GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAGgtttctctac ... tgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGA-TGGGGTGAAGA
EST: gi|151397747|gb|EV267620.1|EV267620
EST:     GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAG                         GGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
genomic: GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAGgtttctctac ... tgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
EST: gi|192320767|gb|FK013857.1|FK013857
EST:     GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAG                         GGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC
genomic: GGCTGGAAATCTACCTTCTTGACCACTGACAAGACCCTCGCTCAACAAAGgtttctctac ... tgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttatggaaaagaagaataaaataaaatattgggtattggaatgtttgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGACAGTCATGGGTCCAATTCCGGGCGTTAAATATGATGAGAGGAGACAACGA
      aaaagaagaataaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taattttctaacttgaaactaaacatgcacacacctttatttgatttatggaaaagaagaataaaataaaatattgggtattggaatgtttgcattgcagGGCGGCTAAACTGGGTATGAAGTTGGAATGGTTGGAAGATGGGGTGAAGACAGTCATGGGTCCAATTCCGGGCGTTAAATATGATGAGAGGAGACAACGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - -aacatgc
- - - - - - - - - - - - - - acacacc
- - - - - - - - - - - - - - - - - - - - - - - - - -aaaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggaatgt