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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCCAGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaaattttatatttttttttttaagaacaaatttgctcatgatgctcttttgctgttttagtacggagcttatgataattactatttactagc...

Basic information

species Glycine max
transcript GLYMA13G38040.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G38040.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv12s0134g00160.t01 (Vitis vinifera), 5'ss of exon 2
TGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCCAGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaaattttatatttttttttttaagaacaaatttgctcatgatgctctttt-----gctgttttagtacggagcttatgataattactatttactagc
 ||||| |||   || || ||||| || |||||||| || || |  || ||| ||||||| |||||||| ||||||||||| |||||||||||||||||||||||| |||  | |   | |     |  |  | ||   ||  | || ||  || |||      |   |||  |  |  | |  ||||  ||||   | ||    
AGCTGGGTTTTCCTCCAAAAGCAAGTACATGTTTGGAAAGGTCAGTATTCAGATCAAGCTCGTGGAGGGCGACTCTGCTGGGACTGTCACTGCTTTCTATgtaagtagaatctcttggtctccccctccatcatcatgctttattatcatcttcatttttattaccaatttcatgtgttgat-gtgatgtttacagctcac----
















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|23730922|gb|BU763570.1|BU763570
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGGCCAACTCACAACGAATTT
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTT
EST: gi|20076055|gb|BQ094847.1|BQ094847
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|209722326|gb|BW665823.1|BW665823
EST:     GCTCAAGCTTGTGGAGGGTGACCTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCCGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: GCTCAAGCTTGTGGAGGGTGAC-TCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|192330868|gb|FK021627.1|FK021627
EST:     AGTTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|254327782|gb|GR834747.1|GR834747
EST:     CTGCT-GAACTGTCACTGC-TTCTAT                         ATGTCATCAGAC-GCCCAACTCACAACGAATTTGATTTCGAG-TTTT-GGC
genomic: CTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|298191789|gb|HO035871.1|HO035871
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|254327781|gb|GR834746.1|GR834746
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|33387513|gb|CA850720.1|CA850720
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|192297480|gb|FG989515.1|FG989515
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|19935068|gb|BQ080098.1|BQ080098
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|7284113|gb|AW596712.1|AW596712
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|12774802|gb|BG239750.1|BG239750
EST:     GCTTGTGGAGGGTGACTCTGCTGGAACTGGCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: GCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|26056322|gb|CA799236.1|CA799236
EST:     TGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
EST: gi|22525223|gb|BU084034.1|BU084034
EST:     AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTAT                         ATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC
genomic: AGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaa ... tgtgatgcagATGTCATCAGACGGCCCAACTCACAACGAATTTGATTTCGAGTTTTTGGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGGATTTGGATCTAAGAGCAAATATATGTTTGGGAAAGTGACCATCCAGCTCAAGCTTGTGGAGGGTGACTCTGCTGGAACTGTCACTGCTTTCTATgtaagtggaaattttatatttttttttttaagaacaaatttgctcatgatgctcttttgctgttttagtacggagcttatgataattactatttactagc

- - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA