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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aattaatcacaacaaattctgcttgtctgtatactgccattattttcttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

Basic information

species Glycine max
transcript GLYMA20G32320.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 2
aattaatcacaacaaattctgcttgtctgtatactgccattattttcttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaa----acagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
      | ||  || ||| |||   | | | |||| | || ||     | | | |  || |  || | |  |   |||| | |    ||  ||  |      || | ||  |  | ||||| |||||||| || ||||| || |||||||| || ||||||||||||||||||||||| || || |||
----gtttactgcacattttgccc-tttat-tactacaataatgcctctatatcatgtt-actagcagctttctttaacgt-gtccatccttttgatgttgtagTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g30520.1 (Oryza sativa), 3'ss of exon 2
-------------aattaatcacaaca-aattctgcttgtctgtat-actgccattattttc-ttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaaac--------agCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
              | || |  |  || ||||||  |  | | | | |   ||||| ||  | ||   |    ||| || ||||   |   |  ||||   | | | || |  |        || | ||  |  | || ||||| |||||||| ||||| || |||||||| || ||||| |||||||||||||| || || || |||
gtttggacttactcactagtgtcttcataattcttttaatatttctcatctccattgttgacattaagttgaattggaatgaaaaggttcatgcccttcgtttttattttaccctattctgtagTTGGTATTGCTTGGAGATTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGCTTTGTCCGTGGTCAGTTTGACCCCACTTCAAAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 3
---aattaatcacaacaaattctgcttgtctgtatactgccattattttcttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
     |    ||  |  |||  ||  |||   |   ||   |  |  |   |   | |     ||         | | |    |  |   || | |   | || | ||  |  | || || || |||||||| ||||| || |||||||| || ||||||||||||||||||||||| || || |||
tatgttagggcatcattaatagtggctgtgatttatctagtaaaacctgaatacctgatt---aacgacttttgttaatgttttcaaccttctcatgttatagTTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 3'ss of exon 2
aattaatcacaacaaattctgcttgtctgtatactgcca----ttattttcttg--tttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaa-acagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
  ||| |  |      |  ||||   | ||||  |||||    |  | |  |||  || ||| |||   |  |   |  |||||| ||     |||||| |   ||| | ||||| ||||| || ||||||||||| ||||| |||||||| || |||||||| ||||||||||||||  | |||||||||
--ttattttct-----tgttgctcagcagtattttgccaagtgtggtataattggtttcaactttgcgtaagacataccactaacttttggattcacttgattgcagTTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAG

upper sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 3'ss of exon 2
------aattaatcacaacaaattctgcttgtctgtatactgccattattttcttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
       |   ||||  | | |   |  |||   |      || | |||    |||  |||       ||   |    | ||  | | |    ||| |     ||||| ||| | || || |||||||||||||| ||||||||||||||||| || ||||||||||| |||||||| || ||||| |||
ctgcaagaaatatcattatagaaattaattgatgg------gcaaatataggattgaataagaaccctaaattatttcagctctcttggtccatcattgtctgcagCTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAG

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|298188274|gb|HO034967.1|HO034967
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|151401597|gb|EV271411.1|EV271411
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGGATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|14009240|gb|BG725844.1|BG725844
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|21887641|gb|BQ740854.1|BQ740854
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|120530730|gb|EH258863.1|EH258863
EST:     NCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: -CAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|33388034|gb|CA851241.1|CA851241
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|120530900|gb|EH259033.1|EH259033
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|213603351|gb|DB966610.1|DB966610
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|14126037|gb|BG790475.1|BG790475
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|11687687|gb|BF595363.1|BF595363
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|58017129|gb|CX703871.1|CX703871
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|151409251|gb|EV279059.1|EV279059
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|192303625|gb|FG998635.1|FG998635
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|151399728|gb|EV269599.1|EV269599
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|13478097|gb|BG507714.1|BG507714
EST:     CAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|19053755|gb|BM732422.1|BM732422
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|6912828|gb|AW394312.1|AW394312
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|6665996|gb|AW277455.1|AW277455
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
EST: gi|6455577|gb|AW186260.1|AW186260
EST:     CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAG                         CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA
genomic: CCAATTCCGAGAATGGTGGAGGGCAGGACGCCAAGAATCTAAGGGTCAAGgtatttgtgt ... cttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG
                           aactaac  putative branch site (score: 1)
               aaaagaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aattaatcacaacaaattctgcttgtctgtatactgccattattttcttgtttaaccttgaaaagaaaccataactaaccttgaatgtcacttaaaacagCTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAG

- - - -cacaaca
- - - - - - - - ttctgct
- - - - - - - - - - - - gtctgta
- - - - - - - - - - - - - - - - -ctgccat
- - - - - - - - - - - - - - - - - - - - - - - - - - - -ccttgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaagaaa