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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggaaagcctataatgttgtattccctcctgagtcattcctattagtatttttaagtttgtttccttttttgacctttttatttactgcaacatcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAGGAGCTGTGCAGTGAACTTGCATTTGACAGCATTAGAGTTGATGTTATCC

Basic information

species Glycine max
transcript GLYMA03G33590.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33590.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G083580_T01 (Zea mays), 3'ss of exon 8
ggaaagcctataatgttgtattccctcctgagtcattcctattagtatttttaagtttgt-ttccttttttgacctttttatttactgcaacatcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAGGAGCTGTGCAGTGAACTTGCATTTGACAGCATTAGAGTTGATGTTATCC
  |  | ||      |   |||| ||  |    |||     ||  | ||  | |   | | ||   || |||  | |   |  |  | |       || ||  ||| |||||||| |||||| ||||  |||||||||| ||| | ||||| ||||| | ||  ||||| ||||||||   ||||||||||||||| || |
ccactgtctcaggcctgccattcactgttata-catgaaggttttttttaatgacgatatgttaacttattgctcatcaaaaatttttctctgaactgcagTCTCTCAATCCTCCAGTATTGATTTTTGTCCAAAGCAAAGAGAGGGCCAAAGAGCTTTACAAAGAACTGGCATTTGATGACATTAGAGTTGATGTAATTC

upper sequence: GLYMA03G33590.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0040g02300.t01 (Vitis vinifera), 3'ss of exon 9
ggaaagcctataatgttgtattccctcctgag-tcattcctattagtatttttaagt---------ttgtttccttttttgacctttttatttactgcaacatcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAGGAGCTGTGCAGTGAACTTGCATTTGACAGCATTAGAGTTGATGTTATCC
          | || ||  |||   |  | || |  | ||||||| || ||| ||||         ||  ||  ||  || |    ||| | |    ||   | |  |||||| | ||||| ||| |  |  | ||  ||||||||||||| ||||| |||||||| | ||  ||||| ||||||||   ||||||||||||||||||||
---------tttat-ttacattttttaattagattgtccctattactaatttcaagtggagtatatttaatttattaattaattcctttgtgtgtcacactttttgctagAGTTTGAATCCACCGATTCTTCTCTTTGTCCAAAGCAAGGAACGTGCAAAGGAGCTCTACACGGAACTGGCATTTGATGACATTAGAGTTGATGTTATCC
















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|19269760|gb|BM886016.1|BM886016
EST:     CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG                         AGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
genomic: CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAGgtaaattgct ... catcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
EST: gi|37996746|gb|CF808335.1|CF808335
EST:     CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG                         AGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
genomic: CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAGgtaaattgct ... catcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
EST: gi|21600899|gb|BQ611230.1|BQ611230
EST:     GAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG                         AGTCTAAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAA
genomic: GAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAGgtaaattgct ... catcttgtagAGTCT-AAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAA
EST: gi|11687673|gb|BF595349.1|BF595349
EST:     CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG                         AGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAA
genomic: CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAGgtaaattgct ... catcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
EST: gi|14989998|gb|BI315671.1|BI315671
EST:     CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG                         AGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
genomic: CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAGgtaaattgct ... catcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
EST: gi|193615021|gb|FK560567.1|FK560567
EST:     CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAG                         AGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG
genomic: CTGGAAGTGAAGAAGGAAAACTTCTAGCAATTCGTCAAAGCTTTGCCGAGgtaaattgct ... catcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttttaagtttgtttccttttttgacctttttatttactgcaacatcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAGGAGCTGTGCAGTGAACTTGCATTTGACAGCATTAGAGTTGATGTTATCC
                     ttttgac  putative branch site (score: 3)
                             tttttatttact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggaaagcctataatgttgtattccctcctgagtcattcctattagtatttttaagtttgtttccttttttgacctttttatttactgcaacatcttgtagAGTCTAAATCCTCCGGTATTGGTTTTCCTCCAAAGCAAGGAGCGTGCCAAGGAGCTGTGCAGTGAACTTGCATTTGACAGCATTAGAGTTGATGTTATCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - -tgttgta
- - - - - - - - - - ttccctc
- - - - - - - - - - - - - - - - -cattcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgcaa