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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcttcacaatttggattcataaatatatgaaatctaattatatttcatttgtctgtattcatacttgactctcatgtggtttgcaaataaatgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA

Basic information

species Glycine max
transcript GLYMA16G31250.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G31250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0059g02250.t01 (Vitis vinifera), 3'ss of exon 2
gcttcacaatttggattcataaatatatgaaatctaattatatttcatttgtctgtattcatacttgactctcatgtggtttgc-----aaataaatgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA
 ||| |   ||||   |    ||||  ||  ||     || | |   |       | | ||  || |  | |    |  ||  |     |||| | | |  |||| || ||||| |||||| ||||| | |||||||||||||| ||||| |||| ||||||| | ||||||||||| |||||||| | ||| |||||||| || 
-cttta-ggtttgctatatggaatagttggcat---gatacaatctgtaaaaacatgtccaccctagcttttttaataattcactatttaaattattttcttcagAACTCTTACTGACAACATGGTGGTGGGAGTATCTAAAGGATTTGAAAAGAGACTTCAATTAGTTGGTGTTGGGTATCGTGCAACGGTTGAAGGAAAAGAC
















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|151407454|gb|EV277269.1|EV277269
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192300606|gb|FG991528.1|FG991528
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCA-TCAAATGCATGGGCTTTTTAG                         GACACTTACAGACGACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192295022|gb|FG986741.1|FG986741
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|15589890|gb|BI674506.1|BI674506
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|120529034|gb|EH257168.1|EH257168
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|31456263|gb|CD398291.1|CD398291
EST:     GGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: GGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|16279798|gb|BI943622.1|BI943622
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTNTAN                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|151398682|gb|EV268553.1|EV268553
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|31460307|gb|CD402275.1|CD402275
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192311171|gb|FK004804.1|FK004804
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192322865|gb|FK014796.1|FK014796
EST:     AAAAGGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|151402351|gb|EV272164.1|EV272164
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192309811|gb|FK000263.1|FK000263
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192317745|gb|FK010163.1|FK010163
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|120529031|gb|EH257165.1|EH257165
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|31459677|gb|CD401705.1|CD401705
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192309812|gb|FK000264.1|FK000264
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|192311186|gb|FK004805.1|FK004805
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|15589906|gb|BI674522.1|BI674522
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|31463718|gb|CD405746.1|CD405746
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
EST: gi|31311287|gb|CD396490.1|CD396490
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCGATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtacttcatt ... atgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgtctgtattcatacttgactctcatgtggtttgcaaataaatgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA
                 acttgac  putative branch site (score: 4)
                                       aaataaatgttatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcttcacaatttggattcataaatatatgaaatctaattatatttcatttgtctgtattcatacttgactctcatgtggtttgcaaataaatgttatcagGACACTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGACAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
gcttcac
- - - - - - - - - - - - - - - - - - - - - - - - - - -tgtattc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttgcaa