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

gttagtccaagctatttccattttgttgcttgaaatagtctgatctatgtttccttttgccgtgatctactcgatcctgaggatgtttttcttgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGTGATACAATCCCTTATATAATTTGCTATGAGCAG

Basic information

species Glycine max
transcript GLYMA01G39430.1
intron # 23
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA01G39430.1 (Glycine max), 3'ss of exon 23
lower sequence: Vv07s0031g00470.t01 (Vitis vinifera), 3'ss of exon 21
----------------gttagtccaagctatttccatt------ttgttgcttgaaatagtctgatctatgt--ttccttttgccgtg-atctactcgatcctgaggatgtt---tttcttgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGTGATACAATCCCTTATATAATTTGCTATGAGCAG
                 ||  ||  |  |||||  |||       ||   ||  || || | |    | | |  ||  || | || |  || ||     | ||||     |    |       |   |||||||||| |||||||||||||   || |||||  |||||||||| | |||||||||| |||||||||| ||||||| |||||||
gtgagttgaacccatctttgatctcatttattttgattactcatctgaaactataattaattttgcttgtatgatttgttctaccattcatttaaatattgctgactgcatagaatgatccattttctagGTGGCACTAAGATTGAAGCAAAGTGGTTACTCAACTGGTTGCTCAGCTGGTGATACAGTCCCTTATATTATTTGCTGTGAGCAG
















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|193303087|gb|FK266653.1|FK266653
EST:     GCCACATGTTCTT                         GTGGCAC-AAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGT
genomic: GCCACATGTTCTTgttagtccaa ... tgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGT
EST: gi|192325409|gb|FK017180.1|FK017180
EST:     CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTT                         GTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGTTTGCTCTGTTGGT
genomic: CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTTgttagtccaa ... tgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGT
EST: gi|208246566|gb|GE044276.1|GE044276
EST:     CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTT                         GTGGCACAAAGATTGAAGCAACAAGG
genomic: CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTTgttagtccaa ... tgatcaatagGTGGCACAAAGATTGAAGCAACAAGG
EST: gi|193379018|gb|FK344352.1|FK344352
EST:     CTAAACCTCCTGAAGCTTATCCAGATGCCAAGAACCAGCCACATGTTCTT                         GTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGT
genomic: CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTTgttagtccaa ... tgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGT
EST: gi|193374950|gb|FK339888.1|FK339888
EST:     CT-AACCTCCTGAAGCTTATCCAGATGCCAAGAACCAGCCACATGTTCTT                         GTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGT
genomic: CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTTgttagtccaa ... tgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGT
EST: gi|208098577|gb|GD894830.1|GD894830
EST:     CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTT                         GTGGCACAAAGATTGAAGCAACAAGG
genomic: CTAAACCTCCTGAAGCTTATCCTGATGCCAAGAACCAGCCACATGTTCTTgttagtccaa ... tgatcaatagGTGGCACAAAGATTGAAGCAACAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtttccttttgccgtgatctactcgatcctgaggatgtttttcttgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGTGATACAATCCCTTATATAATTTGCTATGAGCAG
                                          tcttgat  putative branch site (score: 4)
                                    tgtttttctt  CT-rich tract
                                   atgttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtccaagctatttccattttgttgcttgaaatagtctgatctatgtttccttttgccgtgatctactcgatcctgaggatgtttttcttgatcaatagGTGGCACAAAGATTGAAGCAACAAGGCTACTCTTCTGGTTGCTCTGTTGGTGATACAATCCCTTATATAATTTGCTATGAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG