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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtatgtttaaaataacttgttttgcaacatgtgctattatgttgtggattgatggctttgagtgaatgcagtcttcagcataatattttatttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAGTTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA

Basic information

species Glycine max
transcript GLYMA06G01180.2
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA06G01180.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv03s0038g00160.t01 (Vitis vinifera), 3'ss of exon 3
----tgtatgtttaaaataacttgttttgcaacatgtgctattatgttgtggattgatggctttgagtgaatgcagtcttcagcataatattttatttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAGTTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA
       | || |   ||||       | | |  | ||   | |  ||||| ||| |||   ||     || ||| ||||||||||  || |||  | ||||||||| ||||||||||||||||||||||||   || ||||| |||||||| || ||||| || ||  ||| ||| ||| |||||| |||||| |||||||  
agccaacaagtatcctataaaaaaaacttccatttctggggtaa-attgtgaatt-atgcacttagaccaaagcaatcttcagcatgctacttt--tgattcagGTTTCATCCTGCTTGTATAGACATGACTCCAGAGGAAGCTAAAAGACTCGAGCACTTTTTCTGCCAAAATTGTTCTTCTGAAGATCAAAAGAAGTTGCTG
















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|58019940|gb|CX706682.1|CX706682
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|9985362|gb|BE659470.1|BE659470
EST:     CCTTNNAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|208042660|gb|GD842668.1|GD842668
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTAT
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTAT
EST: gi|254336272|gb|GR842451.1|GR842451
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|58022943|gb|CX709684.1|CX709684
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|208309370|gb|GE106788.1|GE106788
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|31462782|gb|CD404810.1|CD404810
EST:     CCTTACAACCCTGATGACCTAATGGTGCNATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCCAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|193605590|gb|FK559018.1|FK559018
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
EST: gi|17401428|gb|BM178210.1|BM178210
EST:     CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTG                         GTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA
genomic: CCTTACAACCCTGATGACCTAATGGTGCAATGCGAGGGCTGCACTGACTGgtaagtttca ... atttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattgatggctttgagtgaatgcagtcttcagcataatattttatttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAGTTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA
  gattgat  putative branch site (score: 4)
                                         ttttattt  putative PPT
                             ttcagcataatatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtatgtttaaaataacttgttttgcaacatgtgctattatgttgtggattgatggctttgagtgaatgcagtcttcagcataatattttatttattcagGTTCCATCCTGCTTGTATAGACATGACTGTGGAAGAAGCCAAAAGACTTGACCACTTCTTTTGTGAAAGTTGCTCTGCTGAAGGTCAAAAAAAGTTGCAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG