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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtttgagaaaattttcttgcagccagtaaattagtcatcatcattgaattttcataatattgaaaaatgatttaccatttgcacttgttccatgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCAGCTTGAGCGCCAACTGGATTCATCTCTTAAGCAAGTGAGGTCAACAAAG

Basic information

species Glycine max
transcript GLYMA19G04320.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA19G04320.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv14s0083g01050.t01 (Vitis vinifera), 3'ss of exon 3
-------------------------gtttgagaaaattttcttgcagccagtaaattag----tcatcatcattgaattttcataatat--tgaaaaatgatttaccattt--------gcacttgttcc---atgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCAGCTTGAGCGCCAACTGGATTCATCTCTTAAGCAAGTGAGGTCAACAAAG
                          |||   |   |  |  || |     | | || |    |  |  ||||| ||||      ||||  |    ||  |  |  | ||           | |||  ||   ||  |  || ||||||||||| ||||||||||| ||||| || || ||||| |||||||||||||| || ||||| ||  ||||  | |||||||| ||||| || |||
gtgattaagtaccttagttgtggcttttttgaattctgcttctgaaatttctgagttggataattgttttcattcaattacggagatatcttatgcaacaacctgactttattcatgaaatatttgaccctgaatattctagAAACCTTCTTGGGGAAGACTTGGGTCCATTGAACACAAAAGAGCTTGAGCAGCTTGAACGTCAACTTGAGACATCCTTGAAGCAAGTCAGGTCTACTAAG
















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|193537347|gb|FK495838.1|FK495838
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|207806384|gb|GD777391.1|GD777391
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGA-GACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|208166942|gb|GD962004.1|GD962004
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|208282760|gb|GE074670.1|GE074670
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGA-GACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|193431960|gb|FK392932.1|FK392932
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAA-G                         GAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|208197576|gb|GD999805.1|GD999805
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|18733553|gb|BM527677.1|BM527677
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|193422247|gb|FK389692.1|FK389692
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
EST: gi|208071166|gb|GD868441.1|GD868441
EST:     GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAG                         GAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA
genomic: GAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAAAGGACCCAAAGgtgaatttca ... catgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gaattttcataatattgaaaaatgatttaccatttgcacttgttccatgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCAGCTTGAGCGCCAACTGGATTCATCTCTTAAGCAAGTGAGGTCAACAAAG
                                      cttgttcc  CT-rich tract
        ataatattgaaaaatg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgagaaaattttcttgcagccagtaaattagtcatcatcattgaattttcataatattgaaaaatgatttaccatttgcacttgttccatgctgcagGAACCTTCTTGGTGAAGACTTGGGCCCATTAAATACCAAAGATCTTGAGCAGCTTGAGCGCCAACTGGATTCATCTCTTAAGCAAGTGAGGTCAACAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - -tgcagcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcactt