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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaattatttgttgtgttttcggaaatgtagtgttcatactaataactactcggttttggattttgtaattaggcctcattttatgttaatttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAGACGGCAAAAGCTCTTGTTTCTGAGCTTAAACTGATGTCAAAAGAG

Basic information

species Glycine max
transcript GLYMA15G40110.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA15G40110.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g00240.t01 (Vitis vinifera), 3'ss of exon 4
------gtaaaattatttgttgtgttttcggaaatgtagtgttcatactaataactactcggttttggattttgtaattaggcctcatttta--tgttaatttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAGACGGCAAAAGCTCTTGTTTCTGAGCTTAAACTGATGTCAAAAGAG
       |    |||  | || |||||  | |||  |   |  |||| ||||  |||      |    |   |||  ||    || | |       || |||  | ||||| || |||||||| || |||||||| || ||||| || ||||||||||||||  ||||| |||| ||  |||||||||| ||||| |||||||||
gtctgtttttgcttaactcttttgtttg-gtaaacatgaagaacatagtaat--ctaaggaaatgataacactgtgtttgttgctaactaagatcattcattcattcagGTGGTAGCAGCTGGTGCAAACCCTGTTCTAATCACTCGAGGCATTGAGAAGACCACAAAATCTCTAGTGGCTGAGCTTAAGCTGATATCAAAAGAG
















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|10846882|gb|BF069733.1|BF069733
EST:     CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGTGCATTGAGAAG
genomic: CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAGgtaaaattat ... atttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAG
EST: gi|207698046|gb|GD679095.1|GD679095
EST:     CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGG
genomic: CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAGgtaaaattat ... atttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGG
EST: gi|22541364|gb|BU091207.1|BU091207
EST:     CCACGACTTCG-TTGTTCTAGCTCAGGGTCTTATTGCCCAAGGCCTTAAA                         GTTGGTGGAGCTGGGGCCA
genomic: CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAGgtaaaattat ... atttttgcagGTTGTTGCAGCTGGGGCCA
EST: gi|4292240|gb|AI437734.1|AI437734
EST:     CACGACTNCG-TTGTTCTAGCTCAGGGTCTTATTGCCGAAAGCGTTTAAG                         -TTGT-GCAGCTGGG
genomic: CACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTT-AAGgtaaaattat ... atttttgcagGTTGTTGCAGCTGGG
EST: gi|24136477|gb|BU926987.1|BU926987
EST:     CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAG                         GTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAG
genomic: CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAGgtaaaattat ... atttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAG
EST: gi|7926195|gb|AW832221.1|AW832221
EST:     CCACGACTACGGTTGGTCTAGCTCAGGGTCTAATTGCCGAAGGCGTTAAG                         GTTTGT-GCAGCTGGGGCCAACCCTGTGCTCATCACACGGGGCATTGAGAA
genomic: CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAGgtaaaattat ... atttttgcagGTT-GTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAA
EST: gi|213599108|gb|DB962215.1|DB962215
EST:     CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATCGCCGAAGGCGTTAAG                         GTTGTTGCAGCTGGG
genomic: CCACGACTTCGGTTGTTCTAGCTCAGGGTCTTATTGCCGAAGGCGTTAAGgtaaaattat ... atttttgcagGTTGTTGCAGCTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aactactcggttttggattttgtaattaggcctcattttatgttaatttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAGACGGCAAAAGCTCTTGTTTCTGAGCTTAAACTGATGTCAAAAGAG
                                        tgttaat  putative branch site (score: 3)
                                              tttttgc  CT-rich tract
                                tcattttatgttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaattatttgttgtgttttcggaaatgtagtgttcatactaataactactcggttttggattttgtaattaggcctcattttatgttaatttttgcagGTTGTTGCAGCTGGGGCCAACCCTGTGCTCATCACCCGGGGCATTGAGAAGACGGCAAAAGCTCTTGTTTCTGAGCTTAAACTGATGTCAAAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT