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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagatattgtaaaatgtaaagtgatataaagtattagttctaggacactattgtatttataattttgcacttttagattctgtcagtttctttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACAAGGTGTAGTGCTACATACCTGCCTGAAGTGGCCGCCAATGAAG

Basic information

species Glycine max
transcript GLYMA10G24340.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G24340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0101g00100.t01 (Vitis vinifera), 3'ss of exon 3
---aagata-ttgtaaaatgtaaagtgatataaagtattagttctaggacactattgtatttataattttgcacttttagattctgtcagtttctttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACAAGGTGTAGTGCTACATACCTGCCTGAAGTGGCCGCCAATGAAG
   || |||  |   |||| ||   ||| || || | |   |  | |     | ||     | |  |||  |||| | | | | | | | ||||||| |||||||| | ||||||||||||||||||||| ||| ||||||||| |||||| |||||| | ||||| |||||  |||| || ||||| ||| ||||||
tggaaaatagctcctaaatttagcatga-atgaattctggatagtggatt--ttttactgctcttctttcccactgtcataatttattaatttcttt-ttgcagATTGGAAAGCATGGTATAATTATTGAGTTTACTGATCCTGACTATAATACAAGGCGAAGTGCCACATATTTGCCCGAGGTGGCTGCCCATGAAG
















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|209696594|gb|BW666916.1|BW666916
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|298165887|gb|HO008858.1|HO008858
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|192303251|gb|FG995587.1|FG995587
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|209721129|gb|BW659167.1|BW659167
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|298177643|gb|HO027310.1|HO027310
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|298194018|gb|HO040666.1|HO040666
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATCATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|192302476|gb|FG996254.1|FG996254
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATGGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|151397948|gb|EV267821.1|EV267821
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|58017309|gb|CX704051.1|CX704051
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|192319095|gb|FK010631.1|FK010631
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|11274924|gb|BF325249.1|BF325249
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|192313351|gb|FK005123.1|FK005123
EST:     TGTCCCTTCTTGCTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|151395355|gb|EV265226.1|EV265226
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|192294004|gb|FG987173.1|FG987173
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|209721128|gb|BW659166.1|BW659166
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|163927119|gb|EH038550.1|EH038550
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|151395434|gb|EV265311.1|EV265311
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTTCTGATCCTGTCTATAACAC
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTT-CTGATCCTGTCTATAACAC
EST: gi|192313350|gb|FK005122.1|FK005122
EST:     TGTCCCTTCTTGCTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACA
EST: gi|151398285|gb|EV267869.1|EV267869
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|17519784|gb|BM188826.1|BM188826
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
EST: gi|15000051|gb|BI320865.1|BI320865
EST:     TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAG                         ATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA
genomic: TGTCCCTTCTTACTGACTATGAAACTGCTAACCATTACCTTGATTGGGAGgtatgtgctg ... tttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactattgtatttataattttgcacttttagattctgtcagtttctttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACAAGGTGTAGTGCTACATACCTGCCTGAAGTGGCCGCCAATGAAG
                                     tcagtttctttctt  CT-rich tract
        tatttataattttgca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagatattgtaaaatgtaaagtgatataaagtattagttctaggacactattgtatttataattttgcacttttagattctgtcagtttctttcttgcagATAGAAAAGCATGGTATAATTATTGAATTTTCTGATCCTGTCTATAACACAAGGTGTAGTGCTACATACCTGCCTGAAGTGGCCGCCAATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttctgtc