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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtttgttttttgtacctttatgctacatattttttaactacttattttatgctgctgattttaaaatctttgttgtcttatgctgctttctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCA

Basic information

species Glycine max
transcript GLYMA05G32030.1
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 3'ss of exon 6
tgtttgttttttgtacctttatgctacatattttttaac-tacttattttatgctgctgattttaaaatctttgttgtcttatg----ctgctt-tctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCA
    || | |||| |   |      ||  ||||| |||| | || |   |||  |  |  |||  | || | || ||    |||    ||| || ||| | |  || ||||| || || ||||||||||| || ||||| ||||||||||||||| | || ||||| ||||||||  | ||||| || ||  | |||||||| || 
----tgctgtttgaattctcgc-taactgattttataacctgctaagagtata-tatttttttctatatatgtggtgaaacatgatttctgtttgtctctattcagCTATTACTCGCACAACAATGATTACCTGGAAATCTGCCGTTGCTACAAGTCGATTTATGAAATTCCATCAATAAAAGAGGATCCATCAAAGTGGATACCG

upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G64760.2 (Arabidopsis thaliana), 3'ss of exon 6
-------------------------------tgtttgttttttgtacctttatgct-acatattttttaactacttatttta---tgctgctgattttaaaatctttgt--------tgtcttatgctgctttctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCA
                                |   ||| || ||  |   ||  |   ||||| ||   ||    |||||    | |   |  || |   |||||| |        | |  | ||||| ||    | |  ||||||||||| || |||||||| ||  |||| || |||||| |||||||||| |||||||| || || ||||| || ||| |||| |   | |||||||||
gtaagtccttgatttggtttaatacattcttcgccagttattggtgtcaaaatatttgaatattattctcctctgaattttgatttccctttacttctgtgatctttatagtaaaaatataatgtgctgattctgttgtgtagGTATTATTCTCACAACAATGAGTACATTGAGATATGCCGTAGCTACAAGGCGATATATGATATCCCTTCTGTAAAGGAAAACCCAGAACAATGGATTCCA

upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 6
lower sequence: AT5G09900.2 (Arabidopsis thaliana), 3'ss of exon 6
--tgtttgttttttgtacctttatgctacatattttttaactacttattttatgctgctgattttaaaatctttgttgtcttatgctgctttctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCA
  ||  | | | || | |  | |      |  |    | | |  ||  | |    | || || ||    | ||  |   | ||      ||    | |  ||||| ||||| ||||||||||| ||  ||||||| |||||| |||||||||| |||||||| || || || || ||||||   || |   |||||||||| 
attgcat-tatgttatccactgaattctgacgtaccatgattgatttctgtggcattctcatcttttt-tattattaaccataaaaaatttcaactatgtagGTACTATTCTCATAACAATGAGTACATTGAAATCTGCCGTAGCTACAAGGCGATATATGATATCCCTTCAGTAAAAGAAACTCCGGAGCAGTGGATTCCG

upper sequence: GLYMA05G32030.2 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0031g01970.t01 (Vitis vinifera), 3'ss of exon 6
-----tgtttgttttttgtacctttatgctacatattttttaactacttattttatgctgctgattttaaaatctttgttgtcttatgctgctttctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCA
       | |    |||||  | | |||    |||||   |   |  |||| || |  || |   |   ||||   |||  | |  |  | | | || | |  |||||| | ||||| | ||||||||| ||||||||||| ||| |||| ||||| |||||||| || |||||||||| |||||| || ||  ||||||| || 
ctttgcatctaagatttgttgcataatggcctatattgagtccttgtttatatttt--tgtta--taccaaatagatgtcatttggtttttcctact-tgtgtagGTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGCGATATATGAAATCCCATCTGTCAGAGAAGATCCAGCTCAGTGGATACCG

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|5342415|gb|AI794699.1|AI794699
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATT
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATT
EST: gi|120496298|gb|EH224465.1|EH224465
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|19053473|gb|BM732140.1|BM732140
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|37994245|gb|CF805991.1|CF805991
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|26047818|gb|CA784480.1|CA784480
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTAC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTAC
EST: gi|254341094|gb|GR854822.1|GR854822
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|18734862|gb|BM528428.1|BM528428
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|308098502|gb|HO760243.1|HO760243
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|17400997|gb|BM177779.1|BM177779
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|22541281|gb|BU091124.1|BU091124
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|9564218|gb|BE473727.1|BE473727
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|192295223|gb|FG986942.1|FG986942
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAG-C
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|11412649|gb|BF424660.1|BF424660
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|17022950|gb|BM093984.1|BM093984
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
EST: gi|12691513|gb|BG157849.1|BG157849
EST:     ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCG                         GTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC
genomic: ATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaat ... ctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttatgctgctgattttaaaatctttgttgtcttatgctgctttctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCA
        tgctgat  putative branch site (score: 3)
                                      ctgctttctgtttc  putative PPT
             attttaaaatctttgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtttgttttttgtacctttatgctacatattttttaactacttattttatgctgctgattttaaaatctttgttgtcttatgctgctttctgtttcaagGTATTATTCCCATAACAATGATTATCTTGAAATTTGCCGTTGCTACAAGGCAATATATGAGATTCCATCTGTCAAAGAAGACCCTGCCAAGTGGATTCCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA