Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   		13  
 5'  3'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   		30  
 5'  3'   		31  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA

Basic information

species Glycine max
transcript GLYMA09G06890.1
intron # 26
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
lower sequence: AT5G57110.2 (Arabidopsis thaliana), 3'ss of exon 28
-gttgactttct------ttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctttctcta-----tagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA
  |||| |||||      |||     || | |  |||     | | |  |   |  || ||   |    |  | || ||  | ||||| ||      ||||||| ||||| ||||| || ||||| ||||| |||||  ||||  |||| ||||||||||| ||||||||||||||||   |  ||||||| ||  |||
gtttgagtttctgttgcatttagctctttttgaatatctctctctctctaaatattataagt--ttgctcatatatttggcgttttctttaacatacagCTTCTCTGGGTTAATCTGATAATGGACACTCTTGGAGCATTGGCTTTGGCTACTGAACCACCCACTGATCACCTCATGGGGAGGCCTCCAGTTGGCAGAA

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
lower sequence: AT4G29900.1 (Arabidopsis thaliana), 3'ss of exon 28
----------gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctt-tctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA
          || |  ||    | | |||||||    |   |  | ||||| | |   ||     | || |   ||    | |  |||  || | ||||| |||||||| |||||||| ||||||||||| || || || ||  | || ||||| |||||||| |||||| | ||||||||| | || || ||  |||
gttcgaaatagtagttttatactctctctttctcatctgcacaaaagtattcacttcagaa----cttggtaaaaagtcttatcccttacctatgtagCTCCTTTGGGTCAATCTTATAATGGATACTCTTGGGGCTCTTGCTTTAGCCACTGAGCCACCAACCGATCACTTAATGGATCGAGCGCCTGTTGGCAGAA

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
lower sequence: Vv11s0052g00320.t01 (Vitis vinifera), 3'ss of exon 29
----gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgt-tgctttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA
    || | |   |  ||  |   ||| |  |   |   | ||||| ||| |  | |    |    ||      ||| | ||||   || |||| || ||||| |||||||||||||||||||| ||||| || ||  |||| |||||||||||||| |||||||| ||| |  |  ||||||| |||||||
gttggtggcccacccattgctgcctcttgagttgacagttctattatgtc-gtctcatttgtttaactctgtgttgtctactttgcttacagCTCCTCTGGGTTAATCTTATCATGGATACTCTTGGAGCACTTGCATTGGCCACTGAACCACCAACAGATCACCTGATGCACAGGCCTCCAGTTGGTCGAA

upper sequence: GLYMA09G06890.1 (Glycine max), 3'ss of exon 26
lower sequence: EFJ22392 (Selaginella moellendorffii), 3'ss of exon 23
gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA
                                | |    |||  ||  | |    |||      |   | |    | || |||| |||| |||||||| |||||||| ||||||||| |||||||||| ||  | || ||||||||||| || ||  || | |||||| |  | || ||||| || |
-------------------------------gtgagtcgttatctctcgtt---tcatctgttcagtttataagtcgttttctacagCTGCTTTGGGTAAATCTTATTATGGATACTTTGGGAGCGCTCGCTTTAGCCACTGAACCACCTACAGACGACTTAATGGATAGGCCGCCCGTGGGACGCA

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|17020701|gb|BM091735.1|BM091735
EST:     ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAG                         CTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
genomic: ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAGgttgactttc ... ttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
EST: gi|207788931|gb|GD760279.1|GD760279
EST:     ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAG                         CTTCTTTGGGTG
genomic: ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAGgttgactttc ... ttctctatagCTTCTTTGGGTG
EST: gi|193572068|gb|FK532375.1|FK532375
EST:     ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAG                         CTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
genomic: ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAGgttgactttc ... ttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
EST: gi|9820234|gb|BE555744.1|BE555744
EST:     ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAG                         CTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
genomic: ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAGgttgactttc ... ttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
EST: gi|17020693|gb|BM091727.1|BM091727
EST:     ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAG                         CTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
genomic: ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAGgttgactttc ... ttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
EST: gi|207771638|gb|GD744317.1|GD744317
EST:     ATGTTGTTGCCGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAG                         CTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA
genomic: ATGTTGTTGCTGCAGTTTCGTCTGGTGATGTTCCATTAAATGCAGTGCAGgttgactttc ... ttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatgtattaagtcaggatgagccatgatgctaaaatctgttgctttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA
                            tgctaaa  putative branch site (score: 2)
                                    tctgttgctttctct  CT-rich tract
     tattaagt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgactttctttttttctttctaggttatgctcatgtattaagtcaggatgagccatgatgctaaaatctgttgctttctctatagCTTCTTTGGGTGAATCTTATCATGGATACTCTGGGAGCGCTGGCCCTGGCAACTGAACCACCAACTGATCACCTCATGGATCGAACTCCAGTGGGTCGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA