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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagtaatgccattgtttataacattatagaaatataacatcttttaaaaatttcacttaggaaagtcttattatatcgctagaactttgattgccaacttaaaataaaatatatcttatttaaattaattccactttgttatatttcatttgtcatttgcttttgtatagcag

Basic information

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

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA13G06730.2 (Glycine max), 5'ss of exon 2
lower sequence: Vv14s0083g01050.t01 (Vitis vinifera), 5'ss of exon 2
CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgta-cgtagtaatgccattgtttataacattatagaaatataacatcttttaaaaatttcacttaggaaagtcttattatatcgctagaactttgattgccaacttaaaataaaatatatcttatttaaattaattccactttgttatatttcatttgtcatttgcttttgtatagcag
||||||||| ||||| ||||| |||||||| ||||| ||||||||||| |||||||||  |||   ||| |||||||||||    || | ||    |||||| |   | |  ||||   | |  ||| |||  |  | |   ||   ||| |  |  |  |   ||| ||    |     || || |||                                                                     
CATGCTCAAGACACTCGAAAGATACCAAAAATGCAGTTATGGTGCAGTGGAAGTCAGCCGACCCTCCAAGGAGCTTGAGgtggtttaattattatgttgtttctgttaattgagaa---tgatttctcttagtacctgc---tatacaaggca-acaaatttattagcacaccaaag---aatttgaaa---------------------------------------------------------------------
















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|193418766|gb|FK384404.1|FK384404
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         AGCAGCTACCGTGAGTACTTGAAGCTAGAAAGCAAGAT
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcagAGCAGCTACCGTGAGTACTTGAAGCT-GAAAGCAAGAT
EST: gi|193542702|gb|FK499319.1|FK499319
EST:     GTAGCTGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         AGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
genomic: GT-GCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcagAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
EST: gi|193625995|gb|FK576947.1|FK576947
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         AGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcagAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
EST: gi|208331677|gb|GE132390.1|GE132390
EST:     CTATGGTGCAGTTGAAGTCAGCAAAACCTGGCAAAGAGCTTGAG                         AGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
genomic: CTATGGTGCAGTTGAAGTCAGC-AAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcagAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
EST: gi|298176561|gb|HO023148.1|HO023148
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCTGCAAACCTGGCAAAGAGCTTGAG                         C
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcag-
EST: gi|298176561|gb|HO023148.1|HO023148
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCTGCAAACCTGGCAAAGAGCTTGAG                         C
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcag-
EST: gi|207693353|gb|GD674970.1|GD674970
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         AGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGGTTTGAATCTCTTCAA
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcagAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
EST: gi|17020647|gb|BM091681.1|BM091681
EST:     AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGCAG                       
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTT--G-AGgtacgtagta ... tgtatagc
EST: gi|193379920|gb|FK346338.1|FK346338
EST:     AGTGCTGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         C
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcag-
EST: gi|193379920|gb|FK346338.1|FK346338
EST:     AGTGCTGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAG                         C
genomic: AGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcag-
EST: gi|8284985|gb|BE022544.1|BE022544
EST:     AGTCAGCAAACCTGGCAAAGAGCTTGAG                         AGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA
genomic: AGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagta ... tgtatagcagAGCAGCTACCGTGAGTACTTGAAGCTGAAAGCAAGATTTGAATCTCTTCAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTCAAAACACTTGAAAGGTACCAAAAGTGCAGCTATGGTGCAGTTGAAGTCAGCAAACCTGGCAAAGAGCTTGAGgtacgtagtaatgccattgtttataacattatagaaatataacatcttttaaaaatttcacttaggaaagtcttattatatcgctagaactttgattgccaacttaaaataaaatatatcttatttaaattaattccactttgttatatttcatttgtcatttgcttttgtatagcag

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