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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCGGCAACCTTTCTTGCTTTCCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagctgtctgcctgtaaacagtttgtacttatgatttgagattttttgatgttaatgcaaagttcttttgcag

Basic information

species Glycine max
transcript GLYMA07G03180.1
intron # 20
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G03180.1 (Glycine max), 5'ss of exon 20
lower sequence: Vv09s0002g08370.t01 (Vitis vinifera), 5'ss of exon 21
TGCGGCAACCTTTCTTGCTTTCCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaa--cagagctgtctgcctgt----aaacagtttgtac-ttatgatttgagattttttgatgttaatgcaaagttcttt-tgcag
||| ||||| |||||||||||||||||||| |||||||||||||||||||| || |||||||||||  | || || |||||||| ||||| || |||||||||    | || |    |   ||    | |||     ||  |||  |    ||| || || || |  || | |  |||||  |||||
TGCAGCAACATTTCTTGCTTTCCATCCTCAAGATAACAATATTATTGCTATCGGGATGGATGATTCTACAATCCAGATATATAACGTCCGCGTAGATGAGgtagagtacagttaatgggtagttgtcatacatcccatatgttaacaagcaagacttctt-atttggataccattttcttgatgcag

upper sequence: GLYMA07G03180.1 (Glycine max), 5'ss of exon 20
lower sequence: EFJ17248 (Selaginella moellendorffii), 5'ss of exon 21
TGCGGCAACCTTTCTTGCTTTCCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagctgtctgcctgtaaacagtttgtacttatgatttgagattttttgatgttaatgcaaagttcttttgcag
 || ||||| || || ||||| |||||||||||||| ||| |||||||||| || ||||| |||||  |||| || ||||| || || ||||| |||||||||    |     |    ||      ||      ||||   ||   ||||  |  |   | ||||    ||  || |||
AGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGCTATCCATATATACAACGTTCGTGTCGATGAGgtatggaaa--accgatttgc-----gtcatggtttattgattagcatttcattgtaacattgca---ctcgctttcag

upper sequence: GLYMA07G03180.1 (Glycine max), 5'ss of exon 20
lower sequence: EFJ30926 (Selaginella moellendorffii), 5'ss of exon 21
TGCGGCAACCTTTCTTGCTTTCCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgta--acagagctgtctgcctgtaaacagtttgtacttatgatttgagattttttgatgttaatgcaaagttcttttgcag
 || ||||| || || ||||| |||||||||||||| ||| |||||||||| || ||||| |||||   ||| || ||||| || || ||||| |||||||||    | | |  | ||| |    |  |||| |     ||||| |   ||  |||    |||      | ||  || |||
AGCAGCAACATTCCTCGCTTTTCATCCTCAGGATAATAATTTTATTGCTATCGGTATGGAGGATTCGGTTATCCATATATACAACGTTCGTGTCGATGAGgtatggaaaaccgatttgcgt---catggtttat-----tgattagcatttcattg----taacattgcgctcgctttcag

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|6502273|gb|AW203646.1|AW203646
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTGAACTCAAAGGCCATAATAGAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|208111923|gb|GD911041.1|GD911041
EST:     GGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: GGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|26045637|gb|CA783164.1|CA783164
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|15285824|gb|BI469715.1|BI469715
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|4296432|gb|AI442474.1|AI442474
EST:     TAGGCATGGATGATTCCTCTATTCAAA-ATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|6482439|gb|AW201698.1|AW201698
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         G-TAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|207841291|gb|GD810700.1|GD810700
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|26047722|gb|CA784429.1|CA784429
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|4260444|gb|AI416940.1|AI416940
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC
EST: gi|207795116|gb|GD763537.1|GD763537
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGCCATAATAAAAG
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAG
EST: gi|20449020|gb|BQ253144.1|BQ253144
EST:     AGGCATGGATGATTCCTCTATTCAAATATATAATGTCC-TTTTCTTTGAG                         TTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTT
genomic: AGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTT-GATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTT
EST: gi|13252657|gb|BG363560.1|BG363560
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTA
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTA
EST: gi|16346954|gb|BI972549.1|BI972549
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAA
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAA
EST: gi|15337518|gb|BI498174.1|BI498174
EST:     TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAG                         GTTAAAAGTAAACTCAAAGGGCATACTAAAAGAATTACTGGTCTTGCTTTC
genomic: TAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagc ... tcttttgcagGTTAAAAGTAAACTCAAAGGCCATAATAAAAGAATTACTGGTCTTGCTTTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCGGCAACCTTTCTTGCTTTCCATCCTCAGGATAACAATATTATTGCTATAGGCATGGATGATTCCTCTATTCAAATATATAATGTCCGTGTTGATGAGgtaacagagctgtctgcctgtaaacagtttgtacttatgatttgagattttttgatgttaatgcaaagttcttttgcag

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