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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagattaataaatgatttcctataaatggaattgataagacagtaagtaaatttattgaattttgtgatttttggctaaaatattgttcaattgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGATAAGTATGTCACATTTGATGGATTAG

Basic information

species Glycine max
transcript GLYMA03G38930.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G38930.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G09340.1 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------------aagattaataaatgatttcctataaatggaattgataagacagtaagtaaatttattgaattttgt-gatttttggctaaaat------attgttcaattgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGATAAGTATGTCACATTTGATGGATTAG
                                     ||    | |  | |   | | |  || |   |         |   |  | |  | ||| |||  || | |||   || |       ||  |||  |  |  ||||| ||||||| ||| ||| || | || |||||||| ||||| |||||||  ||  |||||||||||||||| || || ||||| || |||||||| ||||
gtcagtcacactttctctaattcttgagcttcctttcatgttcagaaaactcattgttatagggacccactgactgaaactcagctctgatcaatcttgaagagtattgatcaataacatcaaatcattctgtaatttcagGACTTGGCAACAGCCTTTCTCAACGTGCTTGGTAACGAGAAAGCCAGCAGAGAGATATTCAACATCTCGGGGGAGAAATATGTTACCTTTGATGGGTTAG

upper sequence: GLYMA03G38930.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv14s0060g00820.t01 (Vitis vinifera), 3'ss of exon 7
aagattaataaatgatttcctataaatggaattgataagacagtaagtaaatttattgaattttgtgatttttggctaaaatattgttcaattgtgaca-------gGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGATAAGTATGTCACATTTGATGGATTAG
      |  |  | |  |  | | |    ||||  ||    |  |  ||  |||  |||||      |  |||  ||  ||| | ||| || |   |||       |||||||||||| |||||| ||| ||||||| |||||||||| ||||||||| |||| |||||||| || || || || || ||||| ||||||||||| |
----ccaggatgtaacatggtgtgacaaaaatttgtatt-tatgatttatgtttgctgaatggaagcaagttt--ctctaatgtggtttaactcgaacacctcccagGATTTGGCAAAGGCTTTTCTCCTGGTTCTTAGTAATGAGAAAGCCAGCAAGCAAGTCTTCAACATTTCTGGTGAAAAATACGTCACTTTTGATGGATTGG
















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|31468986|gb|CD411014.1|CD411014
EST:     CTATCCCCGGCTCAGGAATACACGATAACCACAACTTNGGTCATGTTAAG                         GATTTGGCCAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: CTATCCCCGGCTCAGGAATACA-GATAACC-CAACTT-GGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|192311714|gb|FK003575.1|FK003575
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GACTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120534123|gb|EH262256.1|EH262256
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTA
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTA
EST: gi|20448825|gb|BQ252949.1|BQ252949
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|10238358|gb|BE807174.1|BE807174
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|31458918|gb|CD400946.1|CD400946
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|19271086|gb|BM887342.1|BM887342
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120531868|gb|EH260001.1|EH260001
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120531132|gb|EH259265.1|EH259265
EST:     TTCCTATCCCCGGCTCAGGAATACAGATTACCCAACTTGGTCAAGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|209718792|gb|BW671993.1|BW671993
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120534655|gb|EH262788.1|EH262788
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|214008768|gb|DB988261.1|DB988261
EST:     CAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTGA-CCAGGTTCTTGGTAATGAGAAGGCCAGCAA
genomic: CAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTT-ATCCAGGTTCTTGGTAATGAGAAGGCCAGCAA
EST: gi|209721698|gb|BW682539.1|BW682539
EST:     GGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: GGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|31468934|gb|CD410962.1|CD410962
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCGAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|17519549|gb|BM188591.1|BM188591
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|209708026|gb|BW657081.1|BW657081
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|9258206|gb|BE346353.1|BE346353
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|14206331|gb|BG840009.1|BG840009
EST:     TCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAAG                         GATTTGGCAAAAGCTTTTATCNCAGGTTCTTGGTAATGAGAAGGCCAGCA
genomic: TCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTT-AAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATC-CAGGTTCTTGGTAATGAGAAGGCCAGCA
EST: gi|213601855|gb|DB982580.1|DB982580
EST:     CAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: CAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|6134478|gb|AW132871.1|AW132871
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|209697178|gb|BW672943.1|BW672943
EST:     CCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: CCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120531334|gb|EH259467.1|EH259467
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120531252|gb|EH259385.1|EH259385
EST:     TTCCTATCCCCGGCTCAGGAATACAGATTACCCTACTTGGTCATGTTAAG                         GATTTGGCCAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|13252610|gb|BG363513.1|BG363513
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATC
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATC
EST: gi|120531009|gb|EH259142.1|EH259142
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120530943|gb|EH259076.1|EH259076
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120496238|gb|EH224405.1|EH224405
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|31457494|gb|CD399522.1|CD399522
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|22541846|gb|BU091689.1|BU091689
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAAGCCAGCCAA
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGC-AA
EST: gi|192311713|gb|FK003574.1|FK003574
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GACTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
EST: gi|120528898|gb|EH257032.1|EH257032
EST:     TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAG                         GATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG
genomic: TTCCTATCCCCGGCTCAGGAATACAGATAACCCAACTTGGTCATGTTAAGgtatgaaatt ... attgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agtaaatttattgaattttgtgatttttggctaaaatattgttcaattgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGATAAGTATGTCACATTTGATGGATTAG
                            ggctaaa  putative branch site (score: 3)
     atttattgaattttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagattaataaatgatttcctataaatggaattgataagacagtaagtaaatttattgaattttgtgatttttggctaaaatattgttcaattgtgacagGATTTGGCAAAAGCTTTTATCCAGGTTCTTGGTAATGAGAAGGCCAGCAAGGAAGTATTCAACATCTCGGGAGATAAGTATGTCACATTTGATGGATTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtg