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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccttcaggcctcattctgcaatattttgagctttatttgccttgagacctggtatggtttaactaaccctttttactacctgttctgacgaacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTTGTTGGTAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG

Basic information

species Glycine max
transcript GLYMA10G33680.1
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 15
lower sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 13
ccttcaggcctcattctgcaatattttgagctttatttgccttgagacctggtatggtttaactaaccctttttactacctgttctgacgaacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTTGTTGGTAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG
             || |  | | ||| || ||  | |   ||   || ||| ||     | || |    || ||   ||  ||| ||    ||    |||||||||||  ||||||| ||||||||||| |||||||| ||||||||| ||||||| || || ||||| ||  || | || || || || |||||||| |
------------gttttctattctttagaactaaaatcctct---gatctgataattgatgacaagaaattgttttaacgagttttggtttac----cagACTCCTGTTTACACAATCGCTTCAAATGCTGGAGTTGAAGGTGCTGTTATTGTTGGCAAGCTCTTGGAGCAAGATAACCCAGACCTCGGTTATGATGCTG

upper sequence: GLYMA10G33680.1 (Glycine max), 3'ss of exon 15
lower sequence: EFJ20894 (Selaginella moellendorffii), 3'ss of exon 13
ccttcaggcctcattctgcaatattttgagctttatttgccttgagacctggtatggtttaactaaccctttttactacc-tgttctgacgaacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTTGTTGGTAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG
                                 |||  ||   | |||    | |   ||   |   | |    |||||  ||||||            |||  ||   | | ||||||||| | ||||||||||| ||||| || || ||||| || || |||| ||||||||||||     |  | || || || || |
--------------------------------gtatg-gcgcggtgacactattttagttgcttttgcgtggccactacaatgttctctt---tgtgatagATGCCCACGTATACAATTGCTGCCAATGCCGGAGTGGAGGGAGCGGTCGTTGTAGGCAAGCTATGGGAACAGAATGACTACAACTTGGGTTACGACGCGG
















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|16277734|gb|BI942535.1|BI942535
EST:     CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
genomic: CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
EST: gi|16278164|gb|BI942759.1|BI942759
EST:     CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
genomic: CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
EST: gi|16284045|gb|BI945876.1|BI945876
EST:     TTACTTTGATCAAAATGAT-GGGGTTCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACATTTGCT
genomic: TAACTTTGATCAAAA-GATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCT
EST: gi|16282089|gb|BI944831.1|BI944831
EST:     CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
genomic: CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
EST: gi|17400780|gb|BM177562.1|BM177562
EST:     CCAACTTTGATCAAAAGATAGGTGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCAGGAGTTGAGGGTGCTGTTGTT
genomic: CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
EST: gi|151399267|gb|EV269138.1|EV269138
EST:     CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
genomic: CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
EST: gi|15813269|gb|BI785544.1|BI785544
EST:     CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
genomic: CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
EST: gi|16276893|gb|BI942097.1|BI942097
EST:     CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAG                         ACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT
genomic: CTAACTTTGATCAAAAGATAGGGGTCCAGATCATCCAAAATGCTTTGAAGgttagtgttt ... aacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacctggtatggtttaactaaccctttttactacctgttctgacgaacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTTGTTGGTAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG
            tttaactaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccttcaggcctcattctgcaatattttgagctttatttgccttgagacctggtatggtttaactaaccctttttactacctgttctgacgaacaatgcagACTCCTGTGCACACAATTGCTTCAAATGCCGGAGTTGAGGGTGCTGTTGTTGTTGGTAAACTATTGGAACAGAATGATCCTGATCTTGGATATGATGCAG

- -tcaggcc
- - - - - - -ttctgca
- - - - - - - - - - - - - - - - - - -tgccttg
- - - - - - - - - - - - - - - - - - - - - - - - -tggtatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgac