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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCCGTTGTTGATAGTAAAATCCTACAATATTGTAGCATAGACAAAAAAGAGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgggaagagatatatcgatccttgcttgttctattttaattagctgaatttgatctacagaagtgagtgttttgtttaacttgaagtggggctttgttttcgttgatgaacag

Basic information

species Glycine max
transcript GLYMA01G42360.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G42360.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv02s0025g04710.t01 (Vitis vinifera), 5'ss of exon 2
TGCCGTTGTTGATAGTAAAATCCTACAATATTGTAGCATAGACAAAAAAGAGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgggaagagatatatcgatccttgcttgt-tctattttaattagctgaatt--tgatctacagaagtg--agtgttttgtttaacttgaagtggggctttgttttcgttgatgaacag
|| ||||||||||  ||||||| | |  || |||||||||||||| ||||| ||||  ||| |||| || ||||| ||||| ||||| ||||||||||| ||   | | |    |  | || | ||      || | | || |||  ||   |   ||  |||| ||    || |  || |    || || | ||||                            
TGACGTTGTTGATTCTAAAATCTTGCCCTACTGTAGCATAGACAAGAAAGAAAAGAGGTCAATTGGGGAGATGGAACAAGATTTTCTTCAGGCACTGCAGgttgattctgttgtat-tttacccatttgcttttatatttaattttgttgcttatcttgctgatttagcatagggccagggccacgtgtatcctgaacctt------------------------
















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|209698918|gb|BW652816.1|BW652816
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|209727737|gb|BW658476.1|BW658476
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|209724933|gb|BW669623.1|BW669623
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|213590959|gb|DB973742.1|DB973742
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|192313508|gb|FK004132.1|FK004132
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|12689209|gb|BG155545.1|BG155545
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|192319988|gb|FK013008.1|FK013008
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|10846589|gb|BF069430.1|BF069430
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
EST: gi|209727237|gb|BW655248.1|BW655248
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAA
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAA
EST: gi|192313523|gb|FK004133.1|FK004133
EST:     AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAA                         GCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT
genomic: AGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgg ... tgatgaacagGCATTCTATTATGAGGGGAAGGCTATTATGTCAAATGAGGAATTTGATAAT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCCGTTGTTGATAGTAAAATCCTACAATATTGTAGCATAGACAAAAAAGAGAAGAAATCAGTTGGTGAAATGGAGCAAGAATTTCTACAGGCACTGCAAgtacgtacgggaagagatatatcgatccttgcttgttctattttaattagctgaatttgatctacagaagtgagtgttttgtttaacttgaagtggggctttgttttcgttgatgaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA