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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtaccagatcaatacatttcacccatatttatgtgcaaagtgtgaaagaaaattttggcaagaagtttttatttgatgctttgtgggtggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT

Basic information

species Glycine max
transcript GLYMA15G04500.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 13
lower sequence: LOC_Os03g16980.2 (Oryza sativa), 3'ss of exon 11
ttgtaccagatcaatacatttcacccatatttatgtgcaaagtgtgaaagaaaattttggcaagaagtttttatttgatgctttgtgggtggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT
       |||| ||||         | | ||   |  ||   |   |  | |  |||  | | |   |  | | ||  | | |  |   |    || ||| | || || ||||  ||     |||  |||   ||||||||||||||||| || || || || || |||||||| ||||| ||||||||| | ||||| |
----gtaagatgaatat--------cctgttgccgaacatcattccatgggatgtttctgaatggcatgctaagtt--tccctgctt--ttaccttgcagTTGATCAACCCAGAGGTTACCGTCACAATGACTGAGAACACTCCTGATGATCCTCGTCAGAGGAAGCCAGACATTACAAAGGCAAAGGAAGTTTTGGGGT

upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 13
lower sequence: AT2G28760.1 (Arabidopsis thaliana), 3'ss of exon 9
ttgtaccagatcaatacatttcacccatatttatgt-gcaaagtgtgaaagaaaattttggcaagaagtttttatttgatgctttgtgggtggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT
                          | |||| |||       | | | | |||  | |  |||  |  |  | |    |   |  || |   |  | ||||||||||| || |  |||||||| |||||||| |||||||| |||||||| ||| | || || ||||||||||| |  ||||| || ||| |  | || |
----------------------gttaacatttttgttatttcatttcacataaatgtgtaacaaataagtaatgtc--gtatataatgagaattgatgcagCTTATTAAACCGGACGTGGAGATAAAGATGGTAGAGAACACACCTGATGATCCAAGGCAGAGGAAACCAGACATAAGCAAAGCTAAAGAAGTTCTTGGTT

upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G59290.1 (Arabidopsis thaliana), 3'ss of exon 11
ttgtaccagatcaatacatttcacccatatttatgtgcaaagtgtgaaagaaaattttggcaagaagtttttatttgatgctttgtgggtggttttt-cagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT
        | |  |  |  || || |  |    ||||  || |     |   | ||   |       |  ||| |   || | |||  ||  |     ||||||||||| ||| |  | ||||| ||||||||||||||||| || ||||| ||| |||| || ||||||||||| |  ||||| || ||| ||||||| |
--------gttagagtcggtttactctaaaagctgtgataaatcctgcatttagttcatgttttggttccttaatgtgtgttgtgtttgtattaaacgcagCTTATTAACCCAAGCATAGAGATAAAGATGGTGGAGAACACACCAGATGATCCAAGACAGAGGAAACCAGACATTAGTAAAGCCAAAGAAGTGTTGGGTT

upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 13
lower sequence: AT3G46440.1 (Arabidopsis thaliana), 3'ss of exon 10
ttgtaccagatcaatacatttcacccatatttatgtgcaaagtgtgaaagaaaattttggcaagaagtttttatttgatgctttgtgggtggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT
                  |   |  |   ||| |    |   | |||   |  | || |  |        |    | |||   ||| |||    || ||||| ||||| ||  |  | ||||| |||||||| |||||||| || ||||| ||| |||| || || |||||||||||||| || || ||| ||||||| |
-----------------gtgagagtctggtttctcgatatgatatgagtaagtacttagaaattcttgggtccgctaatgaaatgttggtttacttgcagCTGATTAACCCGAGCATAGAGATAAAGATGGTTGAGAACACACCGGATGATCCAAGACAGAGGAAGCCAGACATCACAAAGGCTAAAGAAGTGTTGGGAT

upper sequence: GLYMA15G04500.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv06s0004g04390.t01 (Vitis vinifera), 3'ss of exon 12
---ttgtaccagatcaatacatttcacccatatttatgtgcaaagtgtgaaagaaaattttggcaagaagtttttatttgatgctttgtgggt-ggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT
   ||  | ||      |  | | ||     ||||   | ||     |||      ||||||||    |    ||  |  ||||||  ||| | | | || ||||| |||||||| |  |||| ||| || ||||| || |||||||||||||| |||||||| || |||||||||||  | || || || |||||||| || |
gaattcaaacatggttgtgaaatacaga-ggatttcaattcag---ttgagttgttattttggctctgatggattgataaatgcttaatggctcgatgttgcagCTAATTAATCCTGAGGTGGTGATAAAAATGGTAGATAACACTCCTGATGATCCACGACAGAGGAAACCAGACATTTCTAAGGCTAAAGAATTGTTAGGAT

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|10231271|gb|BE800168.1|BE800168
EST:     GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAG                         CTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGAC
genomic: GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAGgtcagtttta ... ggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGAC
EST: gi|213604211|gb|DB974253.1|DB974253
EST:     GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAG                         CTGATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGGG
genomic: GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAGgtcagtttta ... ggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGAC
EST: gi|21676124|gb|BQ628475.1|BQ628475
EST:     GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAG                         CTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGAC
genomic: GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAGgtcagtttta ... ggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGAC
EST: gi|22928257|gb|BU545396.1|BU545396
EST:     GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAG                         CTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGAC
genomic: GTGAATTTACAATGACTGAACTTGCTGAGACAGTTAAAGAGgtcagtttta ... ggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaaagaaaattttggcaagaagtttttatttgatgctttgtgggtggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT
                           atttgat  putative branch site (score: 5)
                                               tttttc  putative PPT
                aagaagtttttattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtaccagatcaatacatttcacccatatttatgtgcaaagtgtgaaagaaaattttggcaagaagtttttatttgatgctttgtgggtggtttttcagCTTATTAATCCAGGTGTGGAGATCAAGATGGTGGAGAACACTCCTGATGACCCACGACAAAGAAAACCAGACATCACAAAAGCAAAGGAATTGTTGGGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - -caataca
- - - - - - - - - -ttcaccc
- - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - -aagtgtg
- - - - - - - - - - - - - - - - - - - - - - - -aagaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgtggg