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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGCTGCTATTCGGGAGGACATCAGTATTAATCTTGGACCGCTGGAGGAGCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtatttttttttttttatctaattagttgctgagtattgtagattccacgtcgactagtgatataatcaaaatagtatatataaacgagagacaaccctc...

Basic information

species Glycine max
transcript GLYMA08G08970.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA08G08970.1 (Glycine max), 5'ss of exon 3
lower sequence: GRMZM2G413652_T01 (Zea mays), 5'ss of exon 4
CATGCTGCTATTCGGGAGGACATCAGTATTAATCTTGGACCGCTGGAGGAGCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttttt-ttttatctaattagttgctgagtattgtagattccacgtcgactagtgatataatcaaaatagtatatataaacgag-agacaaccctc---
||||| |||||||| || |||||||| || |||||||| || ||||||||||| || ||| | | |||||| ||| | || || ||||||||||| |||||||| |||||||  || ||| ||  | |   ||    |  |   ||| |     |    || || |||| |    | | | | || |  | ||    ||  |   
CATGCGGCTATTCGCGAAGACATCAGCATAAATCTTGGTCCTCTGGAGGAGctatcgaacttgtacaaagctgatttgctactctgtgaatctggaggaggtatatttttttacttgatccaa--aataaatgtaggtcat---ttctattgttatgcatgttagaatctacgccggagagacaaccctgcaggttgccggcgag

upper sequence: GLYMA08G08970.1 (Glycine max), 5'ss of exon 3
lower sequence: Vv10s0003g03120.t01 (Vitis vinifera), 5'ss of exon 8
CATGCTGCTATTCGGGAGGACATCAGTATTAATCTTGGACCGCTGGAGGAGCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtatttttttttt---tttatctaattagttgctgagtattgtagat-----tccacgtcgactagtgatataatcaaaatagtatatataaacgagagacaaccctc
|||||||| ||||| || |||||||| || |||||||| || || ||||||||||| ||| | |||||||  || |||||||| ||||||||||||||||||| ||| ||  |      || |  | | ||  | | | || || ||       || ||  | | ||  ||| ||    ||   |  |   ||| |  |  ||     
CATGCTGCAATTCGTGAAGACATCAGCATCAATCTTGGCCCTCTTGAGGAGCTTTCCAACTTGTTCAAAGTTGACATACTTCTCTGTGAATCTGGGGGAGgtaatttgttagtggacacatttcctcactt-ttcatttttataaatgatttctcatgttaagtggt--tatcattggcatcaaac-tggtaacaactggtaat----
















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|193443497|gb|FK404651.1|FK404651
EST:     GCTTTCTAACCTCATCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|208133691|gb|GD931764.1|GD931764
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|298196807|gb|HO041550.1|HO041550
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|208107836|gb|GD902012.1|GD902012
EST:     GCAGATATACTTCTTTGTGAATCGTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTAC
genomic: GCAGATATACTTCTTTGTGAATC-TGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTAC
EST: gi|193360337|gb|FK325121.1|FK325121
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCA
EST: gi|193386654|gb|FK349915.1|FK349915
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|207780309|gb|GD752118.1|GD752118
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|193700674|gb|FK636423.1|FK636423
EST:     CTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATT
genomic: CTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGG-AGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATT
EST: gi|193729781|gb|FK664727.1|FK664727
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|207812518|gb|GD785712.1|GD785712
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|193406312|gb|FK370623.1|FK370623
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGG
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGG
EST: gi|207794539|gb|GD767188.1|GD767188
EST:     GCAGATATACTTCTTTGTGAATCT-GGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|193362412|gb|FK326972.1|FK326972
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
EST: gi|9259040|gb|BE347187.1|BE347187
EST:     GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAG                         ATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA
genomic: GCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtattttttt ... tcttctgcagATAACCTGGCTGCCAATTTCAGCAGGGAATTGGCTGACTATATTATTTACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGCTGCTATTCGGGAGGACATCAGTATTAATCTTGGACCGCTGGAGGAGCTTTCTAACCTCTTCAAAGCAGATATACTTCTTTGTGAATCTGGGGGAGgtatttttttttttttatctaattagttgctgagtattgtagattccacgtcgactagtgatataatcaaaatagtatatataaacgagagacaaccctc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT