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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagaagaatcagatttttctcattatttcaaaacttcagcgatacggtttgttttatatagattttcctttgcaatatactgatacaacttcaattgtatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTCGCTGTGAGCCGAGAGCAAACAAACGAGAACGGAGAGAAGATGTACATCC

Basic information

species Glycine max
transcript GLYMA16G23710.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23710.1 (Glycine max), 3'ss of exon 7
lower sequence: AT5G66190.2 (Arabidopsis thaliana), 3'ss of exon 7
gtcagaagaatcagatttttctcattatttcaaaacttcagcgatacggtttgttttatatagattttcctttgcaatatactgatacaacttcaattgtatgga-----gcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTCGCTGTGAGCCGAGAGCAAACAAACGAGAACGGAGAGAAGATGTACATCC
                            | || ||  | |   || |        || ||   || ||   ||| |  | |  | |     || |||||| ||||     |||||| |||||||||||| | |||||  | || |||||||||||||| ||||| || |||||| ||||||| || |||||||| |||||||| |||||||| |
---------------------------gtacacaagctga--aatccaacccacctt-tactaatgttgtcttgtacaaaaaagctgttg-ttgaattgtgtggataatggcagGAGTTTGAGAAGATGAAGGAGAAGAACCCAGACAACTTCAGGCTGGACTTTGCGGTGAGCAGAGAGCAGACGAACGAGAAGGGAGAGAAAATGTACATTC

upper sequence: GLYMA16G23710.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv18s0001g14450.t01 (Vitis vinifera), 3'ss of exon 7
gtcagaagaatcagat-ttttctcattatttcaaaacttcagcgatacggtttgttttatatagattttcctttgcaatatactg-atacaacttcaattgta--tggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTCGCTGTGAGCCGAGAGCAAACAAACGAGAACGGAGAGAAGATGTACATCC
          | |||| | |||| |   ||||      |   |    |  |||| |     |||| |  | | |   | ||| |  |   ||  |   || |   |  | ||||| |||||||||||| | |||||    || || ||||| ||| ||||||  ||||| ||| ||||||||||||| ||||| || ||||| |||||||| |
---------gtgagatatcttcttacattttcctggtcttcactcccctttttggtgc---tagactaccatgtattaaatattttacgtaatgtattttattcttaaaacagGAGTTTGAGAAGATGAAGGAGAAGGCCCCAGAAAACTTTAGGGTTGACTATGCTGTCAGCAGAGAGCAAACAAATGAGAAGGGCGAGAAAATGTACATTC

upper sequence: GLYMA16G23710.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g03510.t01 (Vitis vinifera), 3'ss of exon 7
---gtcagaagaatcagatttttctcattatttcaaaacttcagcgatacggtttgttttatatagattttcctttgcaatatactgatacaacttcaattgtatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTCGCTGTGAGCCGAGAGCAAACAAACGAGAACGGAGAGAAGATGTACATCC
     | |  | | || ||| || |  | | || || ||   |      ||           || ||  |  | | | ||| |  || |          ||| ||||| |||||||| ||||| ||| | |||||  | ||||| ||||||||| | ||||| || |||||| |||||||| |||| |  || ||||||||||||||||| |
gtgagctggtgcaacatattgtttttctcacttgaatacgatatttgagcg--ccaaacccaatggaagtaacataggaatttgttggtg---------ttggatggaacagGAATTCGAGAAAATGAAGGAGAAGAAGCCTGAGAACTTCAGGTTGGACTTTGCAGTGAGCAGAGAGCAATCAAATGCCAAAGGAGAGAAGATGTACATTC

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|213606827|gb|DB974332.1|DB974332
EST:     CATGGATCTTTTTGGATGTCCCTACAAGCAGCTCATTGCGATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGTGC-T
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTG-ACTT
EST: gi|19452467|gb|BM953877.1|BM953877
EST:     CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|16281497|gb|BI944518.1|BI944518
EST:     CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|8825902|gb|BE209632.1|BE209632
EST:     CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|209707439|gb|BW670952.1|BW670952
EST:     TCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: TCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|120495142|gb|EH223309.1|EH223309
EST:     CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|17518600|gb|BM187642.1|BM187642
EST:     CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|213593048|gb|DB983392.1|DB983392
EST:     TACAAGCAGCTCATTGCTATATATGCTT                         GAATAAGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: TACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|192296690|gb|FG991258.1|FG991258
EST:     CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|209718137|gb|BW657796.1|BW657796
EST:     CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
EST: gi|154204813|gb|EV555075.1|EV555075
EST:     CATGGCTC-TTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAG                         GAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC
genomic: CATGGCTCTTTTTGGGTGTCCCTACAAGCAGCTCATTGCTATATAAGGAGgtcagaagaa ... tatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatatagattttcctttgcaatatactgatacaacttcaattgtatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTCGCTGTGAGCCGAGAGCAAACAAACGAGAACGGAGAGAAGATGTACATCC
                         tactgat  putative branch site (score: 2)
     atagatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagaagaatcagatttttctcattatttcaaaacttcagcgatacggtttgttttatatagattttcctttgcaatatactgatacaacttcaattgtatggagcagGAATTTGAGAAGATGCAAGAGAAATATCCTGACAACTTCAGGCTTGACTTCGCTGTGAGCCGAGAGCAAACAAACGAGAACGGAGAGAAGATGTACATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG