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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatcacaatttagattcataaaaacatcaaatctaactatatttcatttgtccatattcattcttgactctcatgtggttttcaaataaatgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA

Basic information

species Glycine max
transcript GLYMA09G25500.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G25500.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv12s0059g02250.t01 (Vitis vinifera), 3'ss of exon 2
gcatcacaatttagattcataaaaacatcaaatctaactatatttcatttgtccatattcattcttgactctcatgtggtt-----ttcaaataaatgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA
       |  || | |  ||  ||   |     |    || | |   |     ||| | ||  || |  | |    |  ||     || |||| | | |  |||| || ||||| |||||| ||||| | |||||||||||||| |||||||||| ||||||| | ||||||||||| |||||||| | ||| |||||||| || 
---ctttaggtttgctatatggaatagttgg--catgatacaatctgtaaaaacatgtccaccctagcttttttaataattcactatttaaattattttcttcagAACTCTTACTGACAACATGGTGGTGGGAGTATCTAAAGGATTTGAAAAGAGACTTCAATTAGTTGGTGTTGGGTATCGTGCAACGGTTGAAGGAAAAGAC
















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|209726821|gb|BW654886.1|BW654886
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|16279095|gb|BI943255.1|BI943255
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|31307999|gb|CD393202.1|CD393202
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|192295981|gb|FG993374.1|FG993374
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCCTACAGACAACCTGGTGATTGGAGTATTTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|151408947|gb|EV278755.1|EV278755
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|31475052|gb|CD417080.1|CD417080
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCCATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTCAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|16278295|gb|BI942828.1|BI942828
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTNTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|20813993|gb|BQ298471.1|BQ298471
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|18040510|gb|BM308804.1|BM308804
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|192295980|gb|FG993373.1|FG993373
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCCTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|16279097|gb|BI943256.1|BI943256
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|209726822|gb|BW654887.1|BW654887
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|16281722|gb|BI944634.1|BI944634
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|16284551|gb|BI946149.1|BI946149
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACACTTACAGACAACCTGGTGACTGGAGTATCTAAAGGTTTTGACAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
EST: gi|20813870|gb|BQ298348.1|BQ298348
EST:     AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAG                         GACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA
genomic: AAAAAGGCAGTTGAAACCAGAAGGGCCAATCAAATGCATGGGCTTTTTAGgtactttatt ... atgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catttgtccatattcattcttgactctcatgtggttttcaaataaatgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA
                 tcttgac  putative branch site (score: 3)
                                  ttttcaaataaatgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatcacaatttagattcataaaaacatcaaatctaactatatttcatttgtccatattcattcttgactctcatgtggttttcaaataaatgttatcagGACCCTTACAGACAACCTGGTGATTGGAGTATCTAAAGGTTTTGAAAAGAAACTTCAACTTGTTGGTGTTGGTTATCGTGCTATGGTAGAAGGAAACGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAA
- - - - - - - - - ataaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtg