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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttaattctttggccaatattgaactttcaacacctaaaaacaagactgacgattagttatttcacaagatgattttgtttgttttctggtgtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGACTCAGGCTTCGTCATGCTCCCATTACCACCCTCAATATTGTCCAAGCTT

Basic information

species Glycine max
transcript GLYMA13G34560.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G34560.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv19s0014g01390.t01 (Vitis vinifera), 3'ss of exon 9
----ttaattctttggccaatattgaactttcaacacctaaaaa---caagactgacgattagttatttcacaagatgattttgtttgttttctggtgtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGACTCAGGCTTCGTCATGCTCCCATTACCACCCTCAATATTGTCCAAGCTT
      ||||      ||   ||||   || |||| | | | |    ||| |     ||||   ||  |  |||  || ||||     |||||   ||||   |||| | ||||||||||||||  ||||||||||||| || |||||||||||||||||| | || ||| |  |   ||| || ||||| ||| |   |||||| |
ctgaagaatttcagaacctgaattg--tttccaactcatgagagtttcaaaatgatagattgagtaacttccaacttgttttt-----ttttcctctgtattggtagATTGCTGGACACAAGGACCTTCTTGAAGGGGATCCCTACTTGAAGCAAAGACTCCGCCTGCGTGACTCCTACATCACAACCCTAAATGTCTGCCAAGCAT
















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|208243865|gb|GE042988.1|GE042988
EST:     GGGATCAATTGAGGAACAAATATGAAGAAACTAGGAAACTCCTACTTCAG                         GTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
genomic: GGGATCAATTGAGGAACAAATATGAAGAAACTAAGAAACTCCTACTTCAGgtaatgccac ... gtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
EST: gi|208089066|gb|GD888189.1|GD888189
EST:     TCAATTGAGGAACAAATATGAAGAAACTGGGAAACTCCTACTTCAG                         GTGGCTGGACACAAGGAAATTCTTNAAGGGGACCCTTACTTGAAGCAAAGA
genomic: TCAATTGAGGAACAAATATGAAGAAACTAAGAAACTCCTACTTCAGgtaatgccac ... gtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
EST: gi|7589080|gb|AW704862.1|AW704862
EST:     GGGATCAATTGAGGAACAAATATGAAGAAACTAAGAAACTCCTACTTCAG                         GTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
genomic: GGGATCAATTGAGGAACAAATATGAAGAAACTAAGAAACTCCTACTTCAGgtaatgccac ... gtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
EST: gi|208157008|gb|GD956394.1|GD956394
EST:     GGGATCAATTGAGGAACAAATATGAAGAAACTAGGAAACTCCTACTTCAG                         GTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
genomic: GGGATCAATTGAGGAACAAATATGAAGAAACTAAGAAACTCCTACTTCAGgtaatgccac ... gtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
EST: gi|18848873|gb|BM567984.1|BM567984
EST:     GGGATCAATTGAGGAACAAATATGAAGAAACTAAGAAACTCCTACTTCAG                         GTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA
genomic: GGGATCAATTGAGGAACAAATATGAAGAAACTAAGAAACTCCTACTTCAGgtaatgccac ... gtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgacgattagttatttcacaagatgattttgtttgttttctggtgtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGACTCAGGCTTCGTCATGCTCCCATTACCACCCTCAATATTGTCCAAGCTT
 gactgac  putative branch site (score: 2)
                          attttgtttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttaattctttggccaatattgaactttcaacacctaaaaacaagactgacgattagttatttcacaagatgattttgtttgttttctggtgtacctgtagGTGGCTGGACACAAGGAAATTCTTGAAGGGGACCCTTACTTGAAGCAAAGACTCAGGCTTCGTCATGCTCCCATTACCACCCTCAATATTGTCCAAGCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - ctttggc
- - - - - - - - - - - - - -caacacc
- - - - - - - - - - - - - - - - - - aaaacaa