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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatagtggttgtggcatgctaatacattctgatgtatacttctctaatgttgatagctgattgtactttgtatgttaaaattcaaaccagAGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAAAAGAAAGCGCTGTCGAGAACTTCTCCGAGCTTATCAGCAGGCTTTTAAG

Basic information

species Glycine max
transcript GLYMA13G32940.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G32940.1 (Glycine max), 3'ss of exon 18
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 18
gtaatatatagtggttgtggcatgctaatacattctgatgtatacttctctaatgttgatagctgattgtactttgtatgttaaaattcaaaccagAGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAAAAGAAAGCGCTGTCGAGAACTTCTCCGAGCTTATCAGCAGGCTTTTAAG
        |  ||  ||||   |  |||| |  ||  || | |  ||   | | || |     | |   |   | |||  ||   ||      ||| || ||| |||||||||||||||||||||| || ||||||||||| || || || || |||   | |||   |||||  | |  |||||| ||||  | |
-------gtgatgcctgtgtt-ttttaattc-ctcacatctgtgtttggatta-gtagtctcttaaaactgactagtagtttc--atctggtgcagGGAGAACTTGTTTGAAGAAATGTTGCAAGAGCCAGATGAGATAGCAGTTAAGAGGAAACGCACACAAGAGACTCTCCACGTTCTTCAGCAAGCTTACAGG
















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|7640090|gb|AW734399.1|AW734399
EST:     AACAACACCAAGAGAGAGCTGCACAACGTCTTCATTAAAAAGCTATACAG                         AGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAA
genomic: AACAACACCAAGAGAGAGCTGCACAACGTCTTCATTAAAAAGCTATACAGgtaatatata ... ttcaaaccagAGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAA
EST: gi|254339196|gb|GR847913.1|GR847913
EST:     AACAACACCAAGAGAGAGCTGCACAACGTCTTCATTAAAAAGCTATACAG                         AGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAA
genomic: AACAACACCAAGAGAGAGCTGCACAACGTCTTCATTAAAAAGCTATACAGgtaatatata ... ttcaaaccagAGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAA
EST: gi|13477712|gb|BG507480.1|BG507480
EST:     AACAACACCAAGAGAGAGCTGCACAACGTCTTCATTAAAAAGCTATACAG                         AGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAA
genomic: AACAACACCAAGAGAGAGCTGCACAACGTCTTCATTAAAAAGCTATACAGgtaatatata ... ttcaaaccagAGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atacttctctaatgttgatagctgattgtactttgtatgttaaaattcaaaccagAGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAAAAGAAAGCGCTGTCGAGAACTTCTCCGAGCTTATCAGCAGGCTTTTAAG
                               tttgtatgttaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatatagtggttgtggcatgctaatacattctgatgtatacttctctaatgttgatagctgattgtactttgtatgttaaaattcaaaccagAGACAACCTGTTTGAAGAAATGTTGCAAGAACCTGATGAGATAGCTGTGAAAAGAAAGCGCTGTCGAGAACTTCTCCGAGCTTATCAGCAGGCTTTTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT