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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattatgttgaaactggaaacagattatgtactgcttttttgctaaaatttctgcagctatagtatttgcagctcaaatatgaactctgctttttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA

Basic information

species Glycine max
transcript GLYMA07G40370.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40370.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G017624_T01 (Zea mays), 3'ss of exon 4
-----------------------------------------------aattatgttgaaactggaaacagattatgtactgcttttttgctaaaatttctgcagctatagtattt--gcagctcaaatatga--actctgctttttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA
                                               || |||        |   ||     |  ||  |      |     || |         |||  |||||  |||  |     ||||    ||||  | || | || ||||||||||| || || |||| | | || ||||| |||||||| ||||||||  |||| ||||| || | |||||| ||||||||||| || ||||| 
gtaagtttgtcggaaacagctccaatggttacatgctcataacttacaagtattgcatgctttataattccatgagtcttatcgaatccaataagtccacttgaatatcatatttgggcaaattgtgaatgattgttctgtatgtttc-agATTGCATGAACGACTTCAAGAATCCCAAGGTGATGAGGTATTGAAAGCAGAAGCAAGTGCAAAGGTGCACAGGTTTACAGAATGGGCTCTAAAGTGTATC

upper sequence: GLYMA07G40370.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G44090.1 (Arabidopsis thaliana), 3'ss of exon 1
-aattatgttgaaactggaaacagattatgtactgcttttttgctaaaatttctgcagctatagtatttgcagctcaaatatgaactctgctttttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA
   |||||||   | |       | |||| |  || ||   ||  ||   |     | |  |  ||| |  | |     | |    |||     || | |||||||| || |||||||| || || || || ||||| ||  | || ||||||||||||||||| ||||||||||||||||||||||| || |||||||||
ctcttatgttcttattcctcctggtttatct-ttggttagctgggaagggtgagataccctttctatataaatccattttttcccatctcggcgtttccagGTTGCACGAGCGTCTCCAAGAGTGTAACGGTGATGAGGTCCTCAAAGCAGAAGCTGGTGCTAAAGTTCAAAAGTTTACTGAATGGGCACTCAAATGTATA

upper sequence: GLYMA07G40370.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G59910.1 (Arabidopsis thaliana), 3'ss of exon 2
aattatgttgaaactggaaacagattatgtactgcttttttgctaaaattt----ctgcagctatagtatttgcagctcaaatatgaactctgctttttgc-tagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA
    |||||   |   |  | |||  |   | | |   ||    ||| |||    | |    | ||  || || || ||| || ||   | | | |  ||  |||||||||||| |||||||| || ||||| || |||||  |  | || ||||| |||||||| || ||||| ||||| |||||||||||||| |||||||||
----atgttactaaatgtcatagacaaaacaattccgcttaagaaaactttaaatcagtttgtttaacatgtg-agttcatatttggtttgtacatgatgtatagGTTGCATGAGCGTCTCCAAGAGTGCAACGGGGATGAGATTCTAAAAGCAGAGGCTGGTGCCAAAGTTCAGAAGTTCACTGAATGGGCTCTCAAATGTATA

upper sequence: GLYMA07G40370.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv05s0094g01540.t01 (Vitis vinifera), 3'ss of exon 4
aattatgttgaaactggaaacagattatgtactgcttttttgcta--aaatttctgcagctatagtatttgcagctcaa---atatgaactctgctt-tttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA
    |    | |  |    |   |  ||||| |   |   || ||  | || | ||  || ||  |||        |||    | | | |  |||||  ||   ||||||||||| ||||| |||||||||||||| |||||||| |||||||||||||| ||||| ||||| ||||||||||||||||||||||| || ||||| 
---gagacaggagttattgat--accatgtagttgctgactgttattagatgtttgttgc-atgctatccatgtgccaatttgtctcaccattgcttgcttatcagGTTGCATGAGCGTCTTCAGGAATGCAATGGGGATGAAGTCTTGAAGGCAGAAGCAGGTGCCAAGGTCCAAAAGTTTACTGAATGGGCTCTAAAGTGTATT

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|13479390|gb|BG508733.1|BG508733
EST:     CTTGCTGATACAGTTACTGTAATGGCCCAAAG                         GTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGA
genomic: CTTGCTGATACAGTTACTGTAATGGCCCAAAGgtacaacttg ... tttttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGA
EST: gi|254326412|gb|GR841004.1|GR841004
EST:     CAGAGTAGAACAATGAGTCTTGCTGATACAGTTACTGTAATGGCCCAAAG                         GTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGA
genomic: CAGAGTAGAACAATGAGTCTTGCTGATACAGTTACTGTAATGGCCCAAAGgtacaacttg ... tttttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatttctgcagctatagtatttgcagctcaaatatgaactctgctttttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA
 tgctaaa  putative branch site (score: 2)
                                       ctctgctttttgct  putative PPT
             tatagtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattatgttgaaactggaaacagattatgtactgcttttttgctaaaatttctgcagctatagtatttgcagctcaaatatgaactctgctttttgctagGTTGCATGAACGTCTCCAGGAATGCAATGGAGATGAAGTATTGAAGGCAGAAGCTGGTGCTAAGGTTCAAAAGTTTACTGAATGGGCTCTGAAATGTATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG