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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAGAGTTATTGTGGCAGTTGCTGCTGCACCAAAGAAGTCATGGATCCCCGCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaaccatctatctattcaatttatctcttgtttctcctttctttcttatattctttgttggaaattcaagtatgagtaattagtctcactcac...

Basic information

species Glycine max
transcript GLYMA08G07880.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G07880.1 (Glycine max), 5'ss of exon 1
lower sequence: AT1G15820.1 (Arabidopsis thaliana), 5'ss of exon 1
AAAGAGTTATTGTGGCAGTTGCTGCTGC---ACCAAAGAAGTCATGGATCCCCGCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaaccatctatctattcaatttatc--tcttgtttctcctttctttcttatattctttgttggaaattcaagtatgagtaattagtctcactcac
      ||||||| || | ||| |||||    || ||||| || |||||||| || || ||||||||||| |  ||| | ||||| |||||||| ||||||||||||||  |  |   | | |||   | |||      |      | ||   |||    |  | | | |   ||| |  ||  ||   |||   |     | | 
---CTCTTATTGTCGCTGCTGCGGCTGCTCAGCCTAAGAAATCTTGGATCCCTGCCGTTAAAGGTGGTGGCAACTTCCTTGACCCTGAATGGCTCGATGGCTCgtaagtctattctcttttatatctgagttactagcatgaacaatgctgaattttcattcatatctctcataaact--agcttggacaatagattatgataat
















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|213596279|gb|DB961979.1|DB961979
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|298164868|gb|HO010865.1|HO010865
EST:     CTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: CTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAAT-GGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|213614148|gb|DB956788.1|DB956788
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|9902010|gb|BE610978.1|BE610978
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|192313785|gb|FK008749.1|FK008749
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|192298720|gb|FG990986.1|FG990986
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGGCTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|15285813|gb|BI469704.1|BI469704
EST:     GCTGTATTATGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|151397122|gb|EV266995.1|EV266995
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|6916120|gb|AW397650.1|AW397650
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|209726206|gb|BW659571.1|BW659571
EST:     GTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|151400351|gb|EV270165.1|EV270165
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|298166792|gb|HO010231.1|HO010231
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAGTGGCTTGATGGCTC                         GCTACCAGGTGTCTATGGTTTTGACCCACTAGGACTAGGAAGGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|209726205|gb|BW659570.1|BW659570
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|298164108|gb|HO013753.1|HO013753
EST:     CTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: CTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAAT-GGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|298183726|gb|HO028939.1|HO028939
EST:     CTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: CTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAAT-GGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|151401865|gb|EV271678.1|EV271678
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|151404967|gb|EV274781.1|EV274781
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
EST: gi|298183418|gb|HO028631.1|HO028631
EST:     GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTC                         GCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC
genomic: GCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaa ... gcaattgtagGCTACCAGGTGACTATGGTTTTGACCCACTAGGACTAGGAAAGGACCCGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAAGAGTTATTGTGGCAGTTGCTGCTGCACCAAAGAAGTCATGGATCCCCGCTGTAAAAGGTGGTGGGAGTTTCATAGACCCAGAATGGCTTGATGGCTCgtaagttcaaccatctatctattcaatttatctcttgtttctcctttctttcttatattctttgttggaaattcaagtatgagtaattagtctcactcac

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctcactc