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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagtaatgccattgtttataacattatagaaatataacatcttttaaaaatttcacttaggaaagtcttattatatcgctagaactttgattgccaacttaaaataaaatatatcttatttaaattaattccactttgttatatttcatttgtcatttgcttttgtatag

Basic information

species Glycine max
transcript GLYMA13G06730.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G06730.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0083g01050.t01 (Vitis vinifera), 5'ss of exon 2
CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgta-cgtagtaatgccattgtttataacattatagaaatataacatcttttaaaaatttcacttaggaaagtcttattatatcgctagaactttgattgccaacttaaaataaaatatatcttatttaaattaattccactttgttatatttcatttgtcatttgcttttgtatag
||||||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||||  |||   ||| |||||||||||    || | ||    |||||| |   | |  ||||   | |  ||| |||  |  | |   ||   ||| |  |  |  |   ||| ||    |     || || |||                                                                  
CATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAGgtggtttaattattatgttgtttctgttaattgagaa---tgatttctcttagtacctgc---tatacaaggca-acaaatttattagcacaccaaa---gaatttgaaa------------------------------------------------------------------
















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|208244876|gb|GE042067.1|GE042067
EST:     AAGTCAGCAAACCTGGCAAAGAGCTCGAG                         CAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
genomic: AAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
EST: gi|298176561|gb|HO023148.1|HO023148
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCTGCAAACCTGGCAAAGAGCTTGAG                         CAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
EST: gi|207693353|gb|GD674970.1|GD674970
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         -AG--CAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGGTTTGAATCTCTT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
EST: gi|207770397|gb|GD744139.1|GD744139
EST:     A-TGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         CAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTTGAATCTCT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGA-TTTGAATCTCT
EST: gi|193379920|gb|FK346338.1|FK346338
EST:     AGTGCTGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         CAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
EST: gi|193625995|gb|FK576947.1|FK576947
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         -AG--CAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
EST: gi|17020647|gb|BM091681.1|BM091681
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         CAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
EST: gi|208331677|gb|GE132390.1|GE132390
EST:     CTATGGTGCAGTTGAAGTCAGCAAAACCTGGCAAAGAGCTT--G                         -AGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
genomic: CTATGGTGCAGTTGAAGTCAGC-AAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
EST: gi|193418766|gb|FK384404.1|FK384404
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         -AG--CAGCTACCGTGAGTACTTGAAGCTAGAAAGCAAGAT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCT-GAAAGCAAGAT
EST: gi|8284985|gb|BE022544.1|BE022544
EST:     AGTCAGCAAACCTGGCAAAGAGCTT--G                         -AGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT
genomic: AGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... ttttgtatagCAGAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagtaatgccattgtttataacattatagaaatataacatcttttaaaaatttcacttaggaaagtcttattatatcgctagaactttgattgccaacttaaaataaaatatatcttatttaaattaattccactttgttatatttcatttgtcatttgcttttgtatag

- - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT