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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gtgcttttaaaattttccttgtgtatttgtgtgaacacaattcttctgcatccctgtggcaaaattataatctctatatatcttaaactatttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATGCGAG

Basic information

species Glycine max
transcript GLYMA16G33240.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G33240.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G35530.1 (Arabidopsis thaliana), 3'ss of exon 3
--gtgct-tttaaaattttccttgtgtatttgtgtgaacacaattcttctgcatccctgtggcaaaattataatctctatatatcttaa-actatttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATGCGAG
   || |  || ||||||    |||    |    | || |    | || ||| |   | |   |   | | ||| |  ||||  | | | | | | |  |  ||||| ||||||||||||||||| ||||| ||||| || || || ||||||||||| 
ttatgttactttaaatttgaactgt----tctcctaaatatggcttttatgctttgatctcttatgctcagaatgttaatattgcatgatattttgttgtatagGGCGTGCTATGGTGTTTTAAGGTTTGTTATGGAGAGTGGAGCTAAAGGATGCGAA
















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|12496522|gb|BG047106.1|BG047106
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|20812287|gb|BQ296765.1|BQ296765
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTCTTGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|254323366|gb|GR835867.1|GR835867
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|254323365|gb|GR835866.1|GR835866
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|24135528|gb|BU926038.1|BU926038
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|193392562|gb|FK358721.1|FK358721
EST:     CCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGTGGTGCCAAAGGATG
genomic: CCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|21995034|gb|BQ786562.1|BQ786562
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|31460672|gb|CD402700.1|CD402700
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|31459201|gb|CD401229.1|CD401229
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|31460147|gb|CD402535.1|CD402535
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|6566862|gb|AW234494.1|AW234494
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTNTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|254322051|gb|GR837465.1|GR837465
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|209709418|gb|BW668360.1|BW668360
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|4313934|gb|AI461053.1|AI461053
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
EST: gi|254322052|gb|GR837466.1|GR837466
EST:     CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAG                         GGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG
genomic: CAGGCCGAGTCGCTTCGCTACAAGCTCCTCGGCGGCCTCGCTGTTCGCAGgtataacata ... tttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctgcatccctgtggcaaaattataatctctatatatcttaaactatttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATGCGAG
                                             tttatttc  CT-rich tract
               aaaattataatctcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcttttaaaattttccttgtgtatttgtgtgaacacaattcttctgcatccctgtggcaaaattataatctctatatatcttaaactatttatttcagGGCTTGCTATGGTGTTTTAAGATTTGTGATGGAAAGCGGTGCCAAAGGATGCGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
-tgctttt
- - - - - - - ttccttg
- - - - - - - - - - - - - -tgtgtga