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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacagtactttattgtgtaattttctgattttctaatttatatggtattcgttatccattcttgtatcttaatgacatgataagtctatgacctttactttaattgtccacttgattttgagtttttactaaggaatttgtaatgttttttgttgttgtgtataattaatgatctgatctgatatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGG

Basic information

species Glycine max
transcript GLYMA16G23870.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G365035_T01 (Zea mays), 3'ss of exon 6
gtacagtactttattgtgtaattttctgattttctaatttatatggtattcgttatccattcttgtatcttaatgacatgataagtctatgacctttactttaattgtccacttgattttgagtttttactaaggaatttgtaatgttttttgttgttgtgtataattaatgatctgatctgatatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGG
                                                                                  ||    ||||   ||  |||  ||||   ||    |   ||| | | ||   | | || | |  | | |  || |  ||||      | | |   || |  |   |||||||||||   |||||||| ||||| || || || || ||| |||  |||| |     |||||||||||||||  ||||||||||||| |||||||| || |
----------------------------------------------------------------------------------aaaagcatgaatatttattt--ttgtatgctcagct---agtgtctgctt--gtagttatgacttatctgattatactgtac---cgacgttgctatttcttcactgcagGTCTTAAAAAAGAAGCCAGATTTCCGCCGCAAGCCTTGGTCAAACATTACTTCGAGTGCAAAAGATTTTGTACAAAAATTACTAGTTAAGGATCCCCGTG

upper sequence: GLYMA16G23870.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g03420.t01 (Vitis vinifera), 3'ss of exon 6
gtacagtactttattgtgtaattttctgattttctaatttatatggtattcgttatccattcttgtatcttaatgacatgataagtctatgacctttactttaattgtccacttgattttgagtttttactaaggaatttgtaatgttttttgttgttgtgtataattaatgatctgatctgatatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGG
                                                                                  || ||| |   ||| | | |  ||  || ||  || |||  | ||  ||   |   ||||| | |||| | ||  || ||||  ||| || ||||  || | ||   |||||| |    || ||||| |||||||| || |||||||||||||| || || |||| ||| ||||||||||| || || |||||||| || || |||||||
----------------------------------------------------------------------------------aaatcttt---cttgagtgtt-tttccccctctatattggatgtt--ctgttgtgcttgta-ttttttctcttcctgagtatgcttattggtctg-cctaacat--ccagGTCCTTAAGAACAAGCCTGATTTTCGCCGCAAACCATGGCCAACCATAAGCAATGGTGCTAAAGATTTTGTAAAGAAGTTACTAGTGAAAGACCCTCGGG
















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|193420116|gb|FK385554.1|FK385554
EST:     CGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: CGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|193718228|gb|FK653036.1|FK653036
EST:     ACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: ACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|193682134|gb|FK622910.1|FK622910
EST:     CCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: CCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|193573663|gb|FK528351.1|FK528351
EST:     TTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: TTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|207843720|gb|GD813905.1|GD813905
EST:     CGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTCTCGTCGGAAACCATGGCCAACTATTAGT
genomic: CGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|193546146|gb|FK502323.1|FK502323
EST:     ACGCCCA-TTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: ACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|208072384|gb|GD872738.1|GD872738
EST:     GCGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: GCGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|208176277|gb|GD978568.1|GD978568
EST:     GCGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: GCGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|208183682|gb|GD982898.1|GD982898
EST:     GCGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: GCGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|193631037|gb|FK579088.1|FK579088
EST:     ACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: ACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|193567952|gb|FK526529.1|FK526529
EST:     ACTGAGGATGGTATCTTCAAGGAG                         G-CTTACGTAAGAAGCCCGA-TTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: ACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|193544365|gb|FK500310.1|FK500310
EST:     ACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
genomic: ACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGT
EST: gi|208035511|gb|GD837255.1|GD837255
EST:     GCGGAAGGCGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAG                         GTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCAT
genomic: GCGGAAGACGCCCATTTTGGGATAAGACTGAGGATGGTATCTTCAAGGAGgtacagtact ... atatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtaatgttttttgttgttgtgtataattaatgatctgatctgatatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGG
                   ttgtgtataattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacagtactttattgtgtaattttctgattttctaatttatatggtattcgttatccattcttgtatcttaatgacatgataagtctatgacctttactttaattgtccacttgattttgagtttttactaaggaatttgtaatgttttttgttgttgtgtataattaatgatctgatctgatatatgcagGTCTTACGTAAGAAGCCCGATTTTCGTCGGAAACCATGGCCAACTATTAGTAATGCTGCAAAAGATTTTGTGAAAAAATTACTAGTAAAGGATCCTCGGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC