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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCTGGGTGAATAGGTTTGCCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatcaattatagaattatctcaccacaacctggccgttcttgtacttttggcttgaacgcttaaattatgtagttattagtattgccatattttgagaaactctatgattgcactgatgatcataccctggtcactgcag

Basic information

species Glycine max
transcript GLYMA16G29860.2
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G29860.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv16s0050g01050.t01 (Vitis vinifera), 5'ss of exon 3
GCTGGGTGAATAGGTTTGCCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGGgtaaga-atcaattatagaattatctcaccacaacctggccgttcttgtacttttggcttgaacgcttaaattatgtagttattagtattgcc-atattttgagaaactctatgattgcactgatgatcataccctggtcactgcag
| ||||| ||  |||| ||||||||||||||| ||||||||||||| || |||||||||||||| ||||| ||| |||   |  |   | || |   || |      | |   || || ||      |    | | |  |    | | |||  || |||   | |   ||||                                           
GTTGGGTAAACCGGTTCGCCAATGCTGGTGATGCTGCCATGGAAGTAGCAGGAAATACAGCATTGCGGgtgagatatctcctgcattttcat-ttgtcata-ttcaactggaattatatttacaaacta---gttcatttctaattgctataggtcttgtagaaacactgagt------------------------------------------
















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|21888915|gb|BQ742128.1|BQ742128
EST:     CCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatca ... gtcactgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|208286423|gb|GE086509.1|GE086509
EST:     ATGGAAGTGGCTGGAAATACTGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCTAGCAAAGTAGCATACCGG
genomic: ATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatca ... gtcactgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|9203277|gb|BE329501.1|BE329501
EST:     ATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: ATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatca ... gtcactgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|58016567|gb|CX703309.1|CX703309
EST:     CCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatca ... gtcactgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|31466273|gb|CD408301.1|CD408301
EST:     TGGAAGTGGCTGGAAATACAGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
genomic: TGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatca ... gtcactgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG
EST: gi|193523744|gb|FK482203.1|FK482203
EST:     CCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACTGCATTACGG                         TTCCGGCAAGCTAAAACTGAGATTGTATCAGCTAGCAAAGTAGCATACCGG
genomic: CCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatca ... gtcactgcagTTCCGGCAAGCTAAAACTGAGATTGTATCAGCAAGCAAAGTAGCATACCGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCTGGGTGAATAGGTTTGCCAATGCTGGTGATACTGCCATGGAAGTGGCTGGAAATACAGCATTACGGgtaagaatcaattatagaattatctcaccacaacctggccgttcttgtacttttggcttgaacgcttaaattatgtagttattagtattgccatattttgagaaactctatgattgcactgatgatcataccctggtcactgcag

- - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - -  GCTGGA