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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTCGGCGTTGGAGCTGACGGAGTTATCTTTGTCTTGCCTGGCATCAGTGGCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttcttacgaattgttattcctgcatgcttttgattgaatggacataggttctgtttgcatcaattttctttataagtagttatcggaaaggag...

Basic information

species Glycine max
transcript GLYMA03G33080.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33080.1 (Glycine max), 5'ss of exon 2
lower sequence: Vv08s0040g02540.t01 (Vitis vinifera), 5'ss of exon 2
CTTCGGCGTTGGAGCTGACGGAGTTATCTTTGTCTTGCCTGGCATCAGTGGCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttcttacgaattgttattcctgcatgcttttgattgaatggacataggttctgtttgcatcaattttctttataagtagttatcggaaaggag---------
||| ||  |||| |||||||| || ||||| | | |||| || |||| |||||| |||||||| ||||||||||| || |||||||| ||||||||||||||| ||      |  ||||   |  | | |||| |||   |||| ||||       ||||||||  | | |   | | | || | |   |   || |  |         
CTTTGGGATTGGTGCTGACGGTGTGATCTTCGCCATGCCGGGGATCAATGGCACTGATTATACAATGAGGATTTTCAATTCTGATGGCAGTGAGCCTGAGgtaatt------aacaatttcca--cgtacatgttttctgttgagtggatcgtcagtctgtttgt-tgagtagccctgaaaatttgagctaaaaatgtggaaagtaatt
















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|298191755|gb|HO035837.1|HO035837
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|208205313|gb|GE004072.1|GE004072
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTTCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|298187329|gb|HO034478.1|HO034478
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCA
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCA
EST: gi|120532038|gb|EH260171.1|EH260171
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|298195843|gb|HO044234.1|HO044234
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTTGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAG
EST: gi|193479421|gb|FK444206.1|FK444206
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|298175668|gb|HO015187.1|HO015187
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTG
EST: gi|5753437|gb|AI960724.1|AI960724
EST:     GCACCGATTATACCATGAGGANTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGNCA-TGGAGTGCGATGCTTTGCCAAATCTGTTTCTCAGCTTGA
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGG-CAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGA
EST: gi|18041357|gb|BM309651.1|BM309651
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|9986785|gb|BE660893.1|BE660893
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGGTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|298194658|gb|HO043130.1|HO043130
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|208194881|gb|GD989438.1|GD989438
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGGGTGCGATGCT
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCT
EST: gi|298189982|gb|HO032103.1|HO032103
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGA
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGA
EST: gi|298175599|gb|HO015118.1|HO015118
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
EST: gi|298169469|gb|HO020829.1|HO020829
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGC
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGC
EST: gi|192298876|gb|FG987621.1|FG987621
EST:     GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAG                         ATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG
genomic: GCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttc ... ttcttcatagATGTGTGGCAATGGAGTGCGATGCTTTGCCAAATTTGTTTCTCAGCTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTCGGCGTTGGAGCTGACGGAGTTATCTTTGTCTTGCCTGGCATCAGTGGCACCGATTATACCATGAGGATTTTTAACTCTGATGGTAGTGAGCCTGAGgtagttcttcttacgaattgttattcctgcatgcttttgattgaatggacataggttctgtttgcatcaattttctttataagtagttatcggaaaggag

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