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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattcttattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG

Basic information

species Glycine max
transcript GLYMA07G00330.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 9
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattctt---attttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
     || |     |       ||    ||    |||  ||      |       |     || |   | | | | |   |     | | |   || ||  |||| ||||| ||||||| ||| || |||||||| ||| | || || ||||| || || || ||||||||||| ||||| || ||||| |||||||||||||
-----gtttgatcttgaattccatagtttatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactacctgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 13
--ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattctt---attttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
  ||| | |  |  |||| |  | ||    | || ||  ||      |  | |    |    || ||||    ||| || | ||   |||  |   | | |  |||| ||||| ||||||| ||| || |||||||| ||| | || || ||||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||
gtttgatcttgaattctattgtttatttctttgctttaaca----agaatctactcgtgtttctcttgg----tttaattacttcatattacttgaaatatgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCATGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 9
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattctt----attttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
     || |  |||| | | |       |    | || | |||       |   |      |||   |   | | || | ||   |||  |    || ||  |||| ||||| ||||||| ||| || |||||||||||| | || || ||||| || || || ||||||||||| ||||| || ||||| |||||||||||||
-----gtttg-atcttgaattctattgtttatttctttactttaacaagaatctactcgtgtttctcatggtctaattacttcatattacttgaaatcttgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGTATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCCGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 3'ss of exon 2
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattcttattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
     || | | ||| | | |  | ||| || || | |      | ||      ||   || |||   | ||  |||   |||  ||       ||  |||| ||||| ||||||| ||| || |||||||| ||| |||| || ||||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||
-----gtttgtgtcttg-act--ttaaccagaatctac-----ttgggtttctcatggtccattt---gcttcatattgcttgaaat------cttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 7
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattctt---attttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
     || |     |       ||    ||    |||  ||      |       |     || |   | | | | |   |     | | |   || ||  |||| ||||| ||||||| ||| || |||||||| ||| | || || ||||| || || || ||||||||||| ||||| || ||||| |||||||||||||
-----gtttgatcttgaattccatcgtttatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactgcctgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 9
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattctt----attttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
     || |  |||| | | |       |      || | |||       |   |      |||   |   |    | | || | |||  |    || ||  |||| ||||| |||||||  || || |||||||| ||| | || || ||||| ||||| || ||||||||||| ||| | || ||||| |||||||||||||
-----gtttg-atcttgaattccattgtttatggctttactttaaccagaatctactttggtttctcatggtccatttacttcgtattgcttgaaatcttgaagGTCAAGGACAATCCTTCCGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATAAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 9
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattcttattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
     || | | ||| | | |  | ||| || || | |      | ||      ||   |  |||   | ||  |||   |||  ||       ||  |||| ||||| ||||||| ||| || |||||||| ||| ||||  | |||||  |||| || ||||||||||| ||||| || ||||| |||||||||||||
-----gtttgtgtcttg-act--tcaaccagaatctac-----ttgggtttctcatggtctattt---gcttcatattgcttgaaat------cttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCAAAATTTCCCAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA07G00330.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0054g01340.t01 (Vitis vinifera), 3'ss of exon 2
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattctt----attttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
     || |  |||| | | |       | |  | || | |||       |   |      |||   |   | |  | | ||   | |  |    || ||  |||| ||||| ||||||| ||| || |||||||| ||| |||| || ||||| ||||| || ||||||||||| ||||| || ||||| |||||||||||||
-----gtttg-atcttgaattccattgtttgtgtcttgactttaaccagaatctacttgggtttctcatggtctatttacttcatactgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGTTCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

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|8669059|gb|BE190161.1|BE190161
EST:     AAATTGGTCCTACGTTTGCAAAAGGACATGATTTCATCAAGAAGTCTCAG                         GTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCT
genomic: AAATTGGTCCTACGTTTGCAAAAGGACATGATTTCATCAAGAAGTCTCAGgtttgcttaa ... tattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCT
EST: gi|10238321|gb|BE807137.1|BE807137
EST:     ATGATTTCATCAAGAAGTCTCAG                         GTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCT
genomic: ATGATTTCATCAAGAAGTCTCAGgtttgcttaa ... tattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCT
EST: gi|4301834|gb|AI443247.1|AI443247
EST:     AAATTGGTCCTACGTTTGCAAAAGGACATGATTTCATCAAGAAGTCTCAG                         GTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCT
genomic: AAATTGGTCCTACGTTTGCAAAAGGACATGATTTCATCAAGAAGTCTCAGgtttgcttaa ... tattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggcgaaggataacccttttggagatttttatgaattggcattcttattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG
       ggataac  putative branch site (score: 3)
                                         ttcttatttt  putative PPT
                                        attcttattttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttgtctatatctagtagtaatgaactagcattttcattttgtaggcgaaggataacccttttggagatttttatgaattggcattcttattttatagGTGAAGGATAATCCTTTTGGAGATTTTAAAAGTATGCATCGTCATATTTCTAAAGGGTCTTGGACATTCTCTGATCAAGACCATGGATGGCAAGTTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
-tgttgtc
- - - - - - - - - - -aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct