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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaacttgttcgcttattgtttgtttaacctttgttgaatgctgtggaagagaagaagttgatacctagctataatcgtggtttgaaattgttgcactgtgaaatccagtgatcttgtaccttgcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCACTGAAGTTTCTGAACTGTCATTTTTTCAATACCTTTTTCTACAAAAAG

Basic information

species Glycine max
transcript GLYMA17G03010.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03010.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g25370.3 (Oryza sativa), 3'ss of exon 3
gttaaacttgttcgcttattgtttgtttaacctttgttgaatgctgtggaagagaagaagttgatacctagctataatcgtggtttgaaattgttgcactgtgaaatccagtgatcttgtaccttgcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCACTGAAGTTTCTGAACTGTCATTTTTTCAATACCTTTTTCTACAAAAAG
                                         |  | |         |  |||     ||   |  | ||      |||   | | | | | ||| ||     || ||    | |  | ||| ||||| |||||| |||| |||||  ||||||||||||||||    ||||||||    |||||| |||| || || || ||||||||||||||||||||||||
----------------------------------------gtattttattgcttgtgctgttttcttctgtttgaactcaaaaggtgagcatatgggatt-tgacat-----gagctc---cttgacattttcagGTCATAAATTTGTATCTTGAGCTGCTGAAAGAGAGGGAACTGAGAGAACCTAACAAGTTTTTGAAATGCCACTTCTTCAATACCTTTTTCTACAAAAAG

upper sequence: GLYMA17G03010.2 (Glycine max), 3'ss of exon 3
lower sequence: AT3G06910.1 (Arabidopsis thaliana), 3'ss of exon 3
gttaaacttgttcgcttattgtttgtttaacctttgttgaatgctgtggaagagaagaagttgatacctagctataatcgtggtttgaaattgttgcactgtgaaatccagtgatcttgtaccttgcctt-tgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCACTGAAGTTTCTGAACTGTCATTTTTTCAATACCTTTTTCTACAAAAAG
                  ||  | |    | ||   |   | |   |        |||  |||| |  ||  | |  |      ||   |    |    | ||      |   | |||| || |||   | || |||| || ||| | ||  | | |||||||||||| |||||    |||||||||  ||||||||| || ||||||||||||||||| ||||||| ||  |||
-----------------gttagtcgacgcatctaaatctcacgtgatttcttcttagagattga-atataattttcttgtctaattaggacctctatgatttgg----taaaaaccttggactttgttctatgtagGTCATTAATCTTTATATGGTATTGCTGAAAGAAAGGGAAGCTAGAGAACCAAAGAAGTTTCTTAAATGTCATTTTTTCAATACATTTTTCTTCACTAAG
















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|193694405|gb|FK629549.1|FK629549
EST:     CCGGGTGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
genomic: CCGGGTGCATGGTTAAACGATGAGgttaaacttg ... gcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
EST: gi|193542105|gb|FK496217.1|FK496217
EST:     CCGGGTGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
genomic: CCGGGTGCATGGTTAAACGATGAGgttaaacttg ... gcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
EST: gi|193315499|gb|FK280207.1|FK280207
EST:     GACCGGGTGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
genomic: GACCGGGTGCATGGTTAAACGATGAGgttaaacttg ... gcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
EST: gi|208263872|gb|GE065280.1|GE065280
EST:     GACCGGGTGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
genomic: GACCGGGTGCATGGTTAAACGATGAGgttaaacttg ... gcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
EST: gi|208109757|gb|GD902603.1|GD902603
EST:     GACCGGGTGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
genomic: GACCGGGTGCATGGTTAAACGATGAGgttaaacttg ... gcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
EST: gi|208304240|gb|GE104769.1|GE104769
EST:     TGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
genomic: TGCATGGTTAAACGATGAGgttaaacttg ... gcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
EST: gi|193447403|gb|FK414606.1|FK414606
EST:     GACCGGGTGCATGGTTAAACGATGAG                         GTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA
genomic: GACCGGGTGCATGGTTAAACGATGAGgttaaacttg ... gcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggtttgaaattgttgcactgtgaaatccagtgatcttgtaccttgcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCACTGAAGTTTCTGAACTGTCATTTTTTCAATACCTTTTTCTACAAAAAG
                                         ccttgccttt  CT-rich tract
       aaattgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaacttgttcgcttattgtttgtttaacctttgttgaatgctgtggaagagaagaagttgatacctagctataatcgtggtttgaaattgttgcactgtgaaatccagtgatcttgtaccttgcctttgcagGTAATAAATATGTACCTTGAATTGCTGAAAGAGAGGGAGAGAAGAGAACCACTGAAGTTTCTGAACTGTCATTTTTTCAATACCTTTTTCTACAAAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG