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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cgcattcgaaaatgttgaactaactgagatttggaaccctctctctccaccttttcctctactagttagagtttctctaatatctatgtttcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCATGCTGTTTCAGGTTGGTTCTTGGAGCATGTTGAGCCCTTGTTGAAAGTAA

Basic information

species Glycine max
transcript GLYMA12G06530.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G06530.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0004g05030.t01 (Vitis vinifera), 3'ss of exon 6
--cgcattcgaaaatgttgaactaactgagatttgga-accctctctctccaccttttcctctactagttagagtttctctaatatctatgtttcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCATGCTGTTTCAGGTTGGTTCTTGGAGCATGTTGAGCCCTTGTTGAAAGTAA
   |  |   | ||  ||     | || | | |   | |    || | |  |  |||    | |  |  |||      | | | ||| |||| | |||| ||||| |||||| |||||||||| ||||||||||| ||||||||| |||| ||||||||| | |||||||||||||| ||||  || |||||||||||||| |
tttgggtggcataaaattct-tcatctcacactcacatatttccttttttaatttttaaaaccatca--taggaaaattttcacatccatgtctgttaagcagGTGATAAGCCAGCTGGAAAGACGGACTGTTGCTTACCATGAATCAGGTCATGCTGTTGCTGGTTGGTTCTTGGAACATGCGGAACCCTTGTTGAAAGTGA
















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|151408986|gb|EV278794.1|EV278794
EST:     TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAG                         GTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
genomic: TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtcttt ... tcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
EST: gi|5606459|gb|AI900493.1|AI900493
EST:     TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAG                         GTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
genomic: TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtcttt ... tcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
EST: gi|7685136|gb|AW755784.1|AW755784
EST:     TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAG                         GTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
genomic: TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtcttt ... tcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
EST: gi|208117393|gb|GD919091.1|GD919091
EST:     TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAG                         GTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
genomic: TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtcttt ... tcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
EST: gi|23729875|gb|BU763043.1|BU763043
EST:     GAAAAGAGGAACAAG                         GTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
genomic: GAAAAGAGGAACAAGgtatgtcttt ... tcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
EST: gi|22525362|gb|BU084173.1|BU084173
EST:     TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAG                         GTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
genomic: TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtcttt ... tcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
EST: gi|12688251|gb|BG154587.1|BG154587
EST:     TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAA-                         GTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT
genomic: TTGAGGCAGCCATTGATAGGATCATTGGTGGTTTGGAAAAGAGGAACAAGgtatgtcttt ... tcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tccaccttttcctctactagttagagtttctctaatatctatgtttcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCATGCTGTTTCAGGTTGGTTCTTGGAGCATGTTGAGCCCTTGTTGAAAGTAA
                             ctctaat  putative branch site (score: 3)
                                         tgtttctt  putative PPT
                                taatatctatgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cgcattcgaaaatgttgaactaactgagatttggaaccctctctctccaccttttcctctactagttagagtttctctaatatctatgtttcttaaccagGTAATAAGCAAGCTGGAAAGGCGGACTGTTGCCTACCATGAAGCAGGCCATGCTGTTTCAGGTTGGTTCTTGGAGCATGTTGAGCCCTTGTTGAAAGTAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
-gcattcg
- - - - - - tgttgaa
- - - - - - - - - -ctaactg