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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtttgtttcactctatcttttatcctgctttgaggctgttagtgcaatttgaaattttggtggatttattttgtgttggtggtgatttctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAAACATCATACGAGGACAACATAAAGAAAATTGTTGAATTTAGTACG

Basic information

species Glycine max
transcript GLYMA16G27010.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G27010.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g07290.t01 (Vitis vinifera), 3'ss of exon 1
----atgtttgtttcactc-tatcttttatcctg-ctttgaggctgttagtgcaatttgaaattttggtggatttattttgtgttggtggtgatttctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAAACATCATACGAGGACAACATAAAGAAAATTGTTGAATTTAGTACG
    || ||   |||| |   ||  ||  || || |||| | ||  ||  ||  |  |   |||| |    | |||||||||        || || || ||| |||||||||||||| || |||||||| || |||||||||||||||||||  |||||||||||||||||||| |||||||||||||| || || ||||| 
tgttatattatcttcaataacatgcttagtcttgtcttttatgcgatttatgacaagtctgatttagtatcacttattttgt-----caatg-ttcctttgaacagCACAAGTTTGTATTTTGGTACACTCGTCGAACACCTGGAGTTCGAACCCAAACATCATACGAGGACAATATAAAGAAAATTGTGGATTTCAGTACA
















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|298169920|gb|HO018544.1|HO018544
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|57575959|gb|CX548930.1|CX548930
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|17022976|gb|BM094010.1|BM094010
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAATTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|58021292|gb|CX708033.1|CX708033
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|298175937|gb|HO015342.1|HO015342
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|151394261|gb|EV264132.1|EV264132
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|37995997|gb|CF807586.1|CF807586
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACACGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|298171093|gb|HO016125.1|HO016125
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|193547664|gb|FK504609.1|FK504609
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACG
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACG
EST: gi|58020447|gb|CX707189.1|CX707189
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTTTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|16348486|gb|BI974081.1|BI974081
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|298180018|gb|HO025233.1|HO025233
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGA-CACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|192295554|gb|FG988128.1|FG988128
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|208089933|gb|GD890806.1|GD890806
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|209710160|gb|BW681072.1|BW681072
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACACGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|21677127|gb|BQ629478.1|BQ629478
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|207799466|gb|GD769669.1|GD769669
EST:     AGCCGGTCTTCACCCCCTACAAAGA                         CACAAGTTTGTCTTC
genomic: AGCCGGTCTTCACCCCCT-CAA-G-gttcctctct ... ctgtgagcagCACAAGTTTGTCTTC
EST: gi|207799466|gb|GD769669.1|GD769669
EST:     AGCCGGTCTTCACCCCCTACAAAGA                         CACAAGTTTGTCTTC
genomic: AGCCGGTCTTCACCCCCT-CAA-G-gttcctctct ... ctgtgagcagCACAAGTTTGTCTTC
EST: gi|58017961|gb|CX704703.1|CX704703
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|298166699|gb|HO010138.1|HO010138
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|14991741|gb|BI317414.1|BI317414
EST:     AGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGTAGTTCGAAATCAA
genomic: AGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|13789026|gb|BG651617.1|BG651617
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|4397610|gb|AI496607.1|AI496607
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|192326201|gb|FK016288.1|FK016288
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAGGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA
EST: gi|213611709|gb|DB960637.1|DB960637
EST:     TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAG                         CACAAGTTTGTCTTCTGGTACACACGCCGAACACCTGGAGTTCGAAATCAA
genomic: TCGAAGAACGACAAGCTCGTGAACTCAAAGCCGGTCTTCACCCCCTCAAGgttcctctct ... ctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gcaatttgaaattttggtggatttattttgtgttggtggtgatttctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAAACATCATACGAGGACAACATAAAGAAAATTGTTGAATTTAGTACG
                                          tttctgt  CT-rich tract
                    atttattttgtgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtttgtttcactctatcttttatcctgctttgaggctgttagtgcaatttgaaattttggtggatttattttgtgttggtggtgatttctgtgagcagCACAAGTTTGTCTTCTGGTACACGCGCCGAACACCTGGAGTTCGAAATCAAACATCATACGAGGACAACATAAAGAAAATTGTTGAATTTAGTACG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA