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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttggtacaacaattaattaattaataacaagagagactagacttttatgctaattaatgatccatattgatggaagatgtgtttctctttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGTTTTCTGCAGAAGTGAGGGAACAAATATATAAAGTGGCATCTGTCAACCT

Basic information

species Glycine max
transcript GLYMA16G01630.2
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G01630.2 (Glycine max), 3'ss of exon 9
lower sequence: Vv09s0002g00340.t01 (Vitis vinifera), 3'ss of exon 11
gtaagttggtacaa-caattaattaattaataacaagagagactagacttttatgctaattaatga-tccatattgatggaagatgtgtttctctttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGTTTTCTGCAGAAGTGAGGGAACAAATATATAAAGTGGCATCTGTCAACCT
||| |||| |   | ||   || |   | | ||||||| ||   | |  |    |   | || ||| |    ||| |   |  |||||| | |  | | | ||||| ||| | ||||||||||| ||| |||||||||| |||||||| |||||||||   || || ||| ||||||| ||||| |||||||||||||| || ||
gtatgttgatcttatcagccaaattgatcaaaacaagataggaaataactgccagaagaatattgagtttggatttaatcagcatgtgtctttgct-ggcttcagGGTACTATGGGGAGTGTGGAAAAAGAGGAGGTTACATGGAGGTAACTGGGTTTGGCGCTGATGTGCGGGAACAGATATACAAAGTGGCATCTGTGAATCT
















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|9440227|gb|BE440736.1|BE440736
EST:     ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAG                         GCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
genomic: ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAGgtaagttggt ... ttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
EST: gi|193674719|gb|FK620373.1|FK620373
EST:     ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAG                         GCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
genomic: ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAGgtaagttggt ... ttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
EST: gi|208316668|gb|GE115352.1|GE115352
EST:     CAATCAGTCTCCAAAG                         GCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACCGGGT
genomic: CAATCAGTCTCCAAAGgtaagttggt ... ttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
EST: gi|9820372|gb|BE555882.1|BE555882
EST:     ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAG                         GCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
genomic: ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAGgtaagttggt ... ttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
EST: gi|19270346|gb|BM886602.1|BM886602
EST:     ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAG                         GCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
genomic: ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAGgtaagttggt ... ttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
EST: gi|19269497|gb|BM885753.1|BM885753
EST:     ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAG                         GCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
genomic: ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAGgtaagttggt ... ttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
EST: gi|7692142|gb|AW760256.1|AW760256
EST:     ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAG                         GCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT
genomic: ATATGGTGAGAATGATATCACCTTAGTATCTTTTCAATCAGTCTCCAAAGgtaagttggt ... ttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgctaattaatgatccatattgatggaagatgtgtttctctttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGTTTTCTGCAGAAGTGAGGGAACAAATATATAAAGTGGCATCTGTCAACCT
                                    tgtttctctttgtcct  CT-rich tract
       taattaatgat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttggtacaacaattaattaattaataacaagagagactagacttttatgctaattaatgatccatattgatggaagatgtgtttctctttgtcctcagGCTACCACGGGGAGTGTGGGAAACGAGGAGGTTATATGGAGGTGACTGGGTTTTCTGCAGAAGTGAGGGAACAAATATATAAAGTGGCATCTGTCAACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT