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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattaaatattttgttagtctttgtgagattatcgccaactgtgcttgttagttagtctgttttctctaatgcttgtgcgtttgatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGACGTGAGCATGATTGGGCAGTTCGG

Basic information

species Glycine max
transcript GLYMA14G01530.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA14G01530.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ29061 (Selaginella moellendorffii), 3'ss of exon 2
gtaagattaaatattttgttagtctttgtgagattatcgccaactgtgcttgttagttagtctgttttctctaatgcttgtgcgtttgatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGACGTGAGCATGATTGGGCAGTTCGG
                           || || || | ||   | || |||  |||   |  |  || ||   |||||  | | ||       | |||| | ||||| |||||||| || ||||| |||||||| |||||||| |||||||||||| |||| ||||| || || |||  |||||| || ||||| ||
---------------------------gtaagtttctagcttccagttcttcctagccggagttcttacttgtatgctcattcttt-------ctagATCTCGTGAACAACCTCGGCACAATTGCCAGGTCTGGCACCAAGGAGTTCATGGAAGCCTTGGCCGCTGGCGCCGATGTGTCCATGATCGGTCAGTTTGG

upper sequence: GLYMA14G01530.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ17594 (Selaginella moellendorffii), 3'ss of exon 2
gtaagattaaatattttgttagtctttgtgagattatcgccaactgtgcttgttagttagtctgttttctctaatgcttgtgcgtttgatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGACGTGAGCATGATTGGGCAGTTCGG
                           || || || | ||   | || |||  |||   |  |  || ||   |||||  | |  |       | |||| | ||||| |||||||| || ||||| |||||||| |||||||| |||||||||||| |||| ||||| || || |||  |||||| || ||||| ||
---------------------------gtaagtttctagcttccagttcttcctagccggagttcttacttgtatgctcattctct-------ctagATCTCGTGAACAACCTCGGCACAATTGCCAGGTCTGGCACCAAGGAGTTCATGGAAGCCTTGGCCGCTGGCGCCGATGTGTCCATGATCGGTCAGTTTGG
















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|213618380|gb|DB969378.1|DB969378
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213587990|gb|DB957449.1|DB957449
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213597843|gb|DB962196.1|DB962196
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|209700012|gb|BW652924.1|BW652924
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213613889|gb|DB960910.1|DB960910
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|6724508|gb|AW308907.1|AW308907
EST:     GCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: GCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|18041089|gb|BM309383.1|BM309383
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|6501961|gb|AW203334.1|AW203334
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|11274820|gb|BF325146.1|BF325146
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAAGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|209723071|gb|BW662447.1|BW662447
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|6667546|gb|AW278997.1|AW278997
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|213598667|gb|DB964261.1|DB964261
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
EST: gi|17024084|gb|BM095118.1|BM095118
EST:     CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTG                         ATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA
genomic: CAACAACACATTGTCTATCATTGACAGTGGTATTGGCATGACTAAGGCTGgtaagattaa ... gatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actgtgcttgttagttagtctgttttctctaatgcttgtgcgtttgatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGACGTGAGCATGATTGGGCAGTTCGG
          ttagtta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattaaatattttgttagtctttgtgagattatcgccaactgtgcttgttagttagtctgttttctctaatgcttgtgcgtttgatgttccagATTTGGTGAATAACCTCGGTACTATTGCAAGGTCTGGGACCAAGGAATTCATGGAAGCCCTGGCTGCTGGTGCTGACGTGAGCATGATTGGGCAGTTCGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT