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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG

Basic information

species Glycine max
transcript GLYMA08G24160.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01410.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttat---ctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
   |||    |||| | | | | |  | ||| ||    |     | ||| |  |||   || | ||   ||| | |      |||  |  |   || ||  |||| || || ||||||  ||| || |||||||| ||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||
--gtttgatcttgaattccatagtt-tatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactacc--tgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01140.t01 (Vitis vinifera), 3'ss of exon 4
atatttataattgattactaaattagtgtttgttagactattgaacaatat-gtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
|||   | |  | |    |    | |  ||| ||| |  ||       |||      |  || || | |  |   | |  |  |  | | | || ||  |||| |  || ||||||  ||| ||||||| ||| |||||    || |||||||  ||||||||||||||||| ||||  |||||||| |||||||||||||
ataaagaaatctcaagtgttgtcttgaatttcttaaatcatctcttcttatcaaccatcattattttttgatgccacttgaaagagaat-taatcttgcagGTTAGGGACAATCCTTATGGTGATTTTAGAAGCATGTACAAACACATTTCTATGGGATCTTGGACATTCTCAGATCGGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 13
atatttataattgattactaaat-tagtgtttgttagacta-ttgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt---attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
          |||||    || | || ||||| ||    |  || ||||| |   |  | || ||| ||| |   |||| |  |   |||  |   | | |  |||| || || ||||||  ||| || |||||||| ||||| || || ||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||
--------gtttgatcttgaattctattgtttatttctttgctttaacaagaatctactcgtgtttctcttggtttaattacttcatattacttgaaatatgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCATGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01280.t01 (Vitis vinifera), 3'ss of exon 6
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttat---ctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
   |||    |||| | | |  ||  | ||| ||    |     | ||| |  |||   || | ||   ||| | |      ||||   ||   || ||  |||| ||  | ||||||  ||| || |||||||| ||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| || ||||||||||
--gtttgatcttgaattccatcttt-tatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactgc--ttgaaatcttgaagGTCAAGAACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGCCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01220.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaat-tagtgtttgttagacta-ttgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
          |||||    || | || ||||| ||    || || ||||| |   |  | || ||| ||  |   |||| |  |   |||  |    || ||  |||| || || ||||||  ||| || |||||||||||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||
--------gtttgatcttgaattctattgtttatttctttactttaacaagaatctactcgtgtttctcatggtctaattacttcatattacttgaaatcttgaagGTTAAGGACAATCCTTCTGGTGACTTTAAAAGTATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCCGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01470.t01 (Vitis vinifera), 3'ss of exon 2
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
                         || | |||       || | ||  || |   | | |||    | ||   | |    |   |||  |    || ||  |||| || || ||||||  ||| || |||||||| |||||||| || ||||| |||||||| ||||||||||| ||||| |||||||| |||||||||||||
-------------------------gtttgtgtcttgactttaaccagaatctacttgggtttctcatggtc-catttgcttcatattgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01360.t01 (Vitis vinifera), 3'ss of exon 7
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttat---ctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
   |||    |||| | | |   |  | ||| ||    |     | ||| |  |||   || | ||   ||| | |      |||| |  |   || ||  |||| || || ||||||  ||| || |||||||| ||||| || || ||||| || ||||| ||||||||||| ||||| |||||||| |||||||||||||
--gtttgatcttgaattccatcgtt-tatttctttacttcaaccagaatctacttgggtttctcatggtctatttacttcatactgcc--tgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAGGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01520.t01 (Vitis vinifera), 3'ss of exon 2
atatttataattgattactaaattagtgtttgttagactattgaacaatat-gtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
               |  |   || |  ||| | |||  ||       |||      |  || ||   |  |   | |  |  |  | | | |  ||  |||| |  || ||||||  ||| ||||||| ||| |||||| |  | |||| ||| ||||||||||||||||  ||||  |||||||| |||||||||||| 
--------------gtgttgtctt-gaatttctcagatcatctcttcttatcacccatcattatttcttgatgccagttgaaagctaat-taagcttgcagGTTAGGGACAATCCTTCTGGTGATTTTAGAAGCATGTATAGATACATTTTTAAGGGATCTTGGACATTCTTAGATCGGGATCATGGTTGGCAAGTTTCTA

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01230.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
   |||    ||||  | |  |||  |  | | |  ||| || | ||  || |   ||| |||    | ||   | | |  | | |||  |    || ||  |||| || || ||||||   || || |||||||| ||||| || || ||||| |||||||| ||||||||||| ||| | |||||||| |||||||||||||
--gtttgatcttga--attccattgtttatggctttact-ttaaccagaatctactttggtttctcatggtc-catttacttcgtattgcttgaaatcttgaagGTCAAGGACAATCCTTCCGGTGACTTTAAAAGCATGTACCGCCACATTTCCAAAGGATCGTGGACATTCTCAGATAAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01390.t01 (Vitis vinifera), 3'ss of exon 9
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
                         || | |||       |  | ||  || |   | | |||    | ||  || |    |   |||  |    || ||  |||| || || ||||||  ||| || |||||||| ||||||||  | |||||  ||||||| ||||||||||| ||||| |||||||| |||||||||||||
-------------------------gtttgtgtcttgacttcaaccagaatctacttgggtttctcatggtc-tatttgcttcatattgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCAAAATTTCCCAAGGATCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

upper sequence: GLYMA08G24160.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv09s0054g01340.t01 (Vitis vinifera), 3'ss of exon 2
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattctt----attttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
   |||    |||| | | |   | || | |||       || | ||  || |   | | |||    | ||  || | |  |   | |  |    || ||  |||| || || ||||||  ||| || |||||||| |||||||| || ||||| ||||| || ||||||||||| ||||| |||||||| |||||||||||||
--gtttgatcttgaattcca---ttgtttgtgtcttgactttaaccagaatctacttgggtttctcatggtc-tatttacttcatactgcttgaaatcttgaagGTCAAGGACAATCCTTCTGGTGACTTTAAAAGCATGTATCGCCACATTTCCAAAGGTTCGTGGACATTCTCAGATCAGGATCATGGTTGGCAAGTTTCTG

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|209716122|gb|BW662320.1|BW662320
EST:     AAATTGGTCCTACACTTGCAAAAGGACATGACTTCATCAAGAAGTCTCAG                         GTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCT
genomic: AAATTGGTCCTACACTTGCAAAAGGACATGACTTCATCAAGAAGTCTCAGgtttgcttaa ... tattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caatatgtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG
                                         ttcttatttt  CT-rich tract
           ttgtttttatctagta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atatttataattgattactaaattagtgtttgttagactattgaacaatatgtttgttgtttttatctagtaataatgaactggcattcttattttatagGTAAAAGATAATCCTCTTGGAGATTTTAAAAGTATGTATCGTCATATTTCTAAAGGATCTTGGACATTCTCTGATCAAGATCATGGATGGCAAGTTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattct