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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcctcttaaaaatgttgcagtgaagagtgtcaaattctcatgtcaagtttttcttattttggcactggttatacttccatttagaatttggaattgctattactccttgaccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGCTCCCGTGTTTCGGTCTACTCAACGTGCAGAAAAACGGAAGGAG

Basic information

species Glycine max
transcript GLYMA20G34780.1
intron # 3
splice site 3'
intron type U12 (go to U12 genes for details)

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|15199929|gb|BI424081.1|BI424081
EST:     GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT                         AACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
genomic: GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAATgtatcctctt ... ccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
EST: gi|5687837|gb|AI940816.1|AI940816
EST:     GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT                         AACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTG
genomic: GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAATgtatcctctt ... ccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTG
EST: gi|10236980|gb|BE805868.1|BE805868
EST:     GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT                         AACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
genomic: GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAATgtatcctctt ... ccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
EST: gi|192309425|gb|FK000941.1|FK000941
EST:     GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT                         AACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
genomic: GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAATgtatcctctt ... ccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
EST: gi|17153596|gb|BM143529.1|BM143529
EST:     GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAAT                         AACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
genomic: GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAATgtatcctctt ... ccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC
EST: gi|192331631|gb|FK023449.1|FK023449
EST:     GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCA-T                         AACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACA-CTGTTGCTTCTGC
genomic: GATAACAAGAAGCATCCTGATGATGATGATTCTTGTTCAGTTGCTTCAATgtatcctctt ... ccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggttatacttccatttagaatttggaattgctattactccttgaccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGCTCCCGTGTTTCGGTCTACTCAACGTGCAGAAAAACGGAAGGAG
 ctccttgac  putative branch site 
             atttagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatcctcttaaaaatgttgcagtgaagagtgtcaaattctcatgtcaagtttttcttattttggcactggttatacttccatttagaatttggaattgctattactccttgaccgtgtaaagAACTGCAGCTTCTGTGAGATCAATCAAGTCCAGGACAACTGTTGCTTCTGCTCCCGTGTTTCGGTCTACTCAACGTGCAGAAAAACGGAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG