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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatatggggctaatgtgtttatggttggcattatgaacttgtaatgaagattactggtgttgtggaaagttttctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

Basic information

species Glycine max
transcript GLYMA08G46850.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G46850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
attatatggggctaatgtgtt-tatggttggcattatgaacttgtaatgaagattactggtgttgtggaaagttttctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
  | | ||  | |   ||| | ||  |||   || | ||    ||  |     ||  | | ||| |||  |  ||        || | ||||||  ||||||||||| ||||||||||| ||||| || |  ||||| ||||| ||  ||||||| |  ||||| || || |||||||| |||||||  ||||| ||||||
tctttgtgaagattcagtgatgtagcgttttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggct-tttgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT

upper sequence: GLYMA08G46850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT5G48760.1 (Arabidopsis thaliana), 3'ss of exon 1
---------------------------------------------------------------------------------------------attatatggggctaatgtgtttatggttggcatt--atgaacttgtaatgaagattactggtgttgtggaaagtttt--ctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
                                                                                              ||||  | |  | || |||   || ||   |||  |||   ||| ||||| ||||   | |      |  | |  |   ||  | |  | ||  | | || || ||||| ||||||||||| ||||| || |  |||||  | ||||| |||||||| || || ||  ||||| |||| |||||||||| |||||||||||| 
gttcgtatatcaatctctcttatctctccaattagatgaggtttcgagaaattgatggttcttgctctgtatggattaagtttgtgtttgatacttatgagtgaatcatttgtggttgatttcaattcaatgcttttgaaatgatgatt-tagatagcagagtgattcatagttgttatgtgttttgatttgtgaagTATGATTCCACACAAGACGAAGCGTGGAGCTGCTGCATTAGCACGTCTGAAGGTATATGAAGGTGTTCCTACTCCATATGACAAGATCAAGAGGATGGTC

upper sequence: GLYMA08G46850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 3'ss of exon 1
------attatatggggctaatgtgtttatggttggcattatgaacttgtaatgaagattactggtgttgtggaaagttttctgagaaggatgtttgt-gtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
      |   | ||    |  ||   | |||  ||   ||| ||| |||||     | ||  | ||||  ||||   |||    |   |    |||||  | | ||||||||| ||||||||||| ||||| || |  ||||||||||||||  |||||||||  |||||  | || |||||||||||||||  |||||| ||||| 
atggtcagcttttgatctttgtgcaatgatgtctg-tgttaggaa-ttgtat----gtttgatagtgtgatggaggatttga-aatgtgatcatttgtcatttacagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCTCTTGCACGTTTGAAGGTGTTTGAGGGAGTACCACCTCCTTATGACAAGGTCAAGAGAATGGTC

upper sequence: GLYMA08G46850.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
attatatggggctaatgtgtttatggttggcattatgaacttgta-atgaagattact---ggtgttgtggaaagttttctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
    | ||| ||   |||   | |  ||  | | || |  |   | |   || ||| |        |||    | |    |     || | | | |   || |||||||| || |||||||| ||||| || | ||| || ||||||||| ||||||  || ||||| || ||||| || ||||| ||||  ||||||||||| 
--attttggtgcc--tgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC

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|208151829|gb|GD948262.1|GD948262
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|209719538|gb|BW669175.1|BW669175
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|208049557|gb|GD848460.1|GD848460
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAGGCGCGGG-AAGCGTGCTCTTGCACGACTGA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGC-TGCTCTTGCACGACTGA
EST: gi|298171760|gb|HO021352.1|HO021352
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|209719537|gb|BW669174.1|BW669174
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|298173139|gb|HO020123.1|HO020123
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|298188599|gb|HO035292.1|HO035292
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|298179434|gb|HO027905.1|HO027905
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|298195963|gb|HO044354.1|HO044354
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|193480555|gb|FK446317.1|FK446317
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTT
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTT
EST: gi|58024885|gb|CX711626.1|CX711626
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|151394249|gb|EV264120.1|EV264120
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|213615010|gb|DB957048.1|DB957048
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|7041647|gb|AW471599.1|AW471599
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|193633372|gb|FK582944.1|FK582944
EST:     CCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|15813016|gb|BI785291.1|BI785291
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|193689049|gb|FK630070.1|FK630070
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGAATAACCACACAAGACAAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGA-TA-CCACACAAGACAAA
EST: gi|193558701|gb|FK512916.1|FK512916
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|207771408|gb|GD745291.1|GD745291
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAA
EST: gi|207730094|gb|GD706884.1|GD706884
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCATTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAG
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAG
EST: gi|207800118|gb|GD768347.1|GD768347
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|41146366|gb|CK606577.1|CK606577
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|13790079|gb|BG652670.1|BG652670
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|9899592|gb|BE608560.1|BE608560
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
EST: gi|213599333|gb|DB972275.1|DB972275
EST:     CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGG                         GATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA
genomic: CCCATCCATTTCCGTGCACCCGGCAAGATCTTCTGGCGCACCGTTCGTGGgtcagcactc ... gtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaagattactggtgttgtggaaagttttctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT
                      aaagtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatatggggctaatgtgtttatggttggcattatgaacttgtaatgaagattactggtgttgtggaaagttttctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - gctaatg
- - - - - - - - - - - -tggttgg
- - - - - - - - - - - - - - - - -tatgaac
- - - - - - - - - - - - - - - - - - - - - - aatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggtgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ggatgtt