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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaataccctgtcataactttttttaccaaactagattgtagttattgtttgtattgaattcactaacaagctgctctaatttccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGGATGTCTGAAGCACATGCGAGAATGCATCTCAGGCAACATGTTACACAAG

Basic information

species Glycine max
transcript GLYMA17G03920.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 15
-----------------------------------gtaataccctgtcataactttttttaccaaactagattgtagttattgtttgtattgaattcactaacaagctgctcta---atttccttgtat-agCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGGATGTCTGAAGCACATGCGAGAATGCATCTCAGGCAACATGTTACACAAG
                                    |  || |   |  | |  | | || || || | |||  |  |   | |    | || |   || |||| | |   | |   |||| ||||| | |||| || ||||||||||||||||| |||||||| || ||||| || ||  ||||||| || |||||||| || |||||| | |||    | ||  | || |
gtaagatatccttgtttcttgtccatatcaaatgcatcttatcaaatacttaaatatcttgccgaattggatattgatacctatgaaaactggaa--accaacatgatatccaacctattttcttgtttcagCATGGTCAAGGAGTCCCTATTGCCGTAAGGCATATCGAATCCATTATTCGGATGTCAGAGGCACATGCAAGGATGCATTTGAGGAGCTACGTGTCTCAGG

upper sequence: GLYMA17G03920.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 14
gtaataccctgtcataactttttttaccaaactagattgtagttattgtttgtattgaattcactaacaagctgctctaatttccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGGATGTCTGAAGCACATGCGAGAATGCATCTCAGGCAACATGTTACACAAG
          || | |  ||   || | ||  | || |   |  | || |  | || | || |  | |    ||   ||   | | ||| ||||| |||||||||||||| || || |||||||| || |||||||||||| ||||||||||||||||||| |||||||| ||||| || |||||||| || |
----------gtgagactttcccttgctaatttcgagttagg--actgatcttgtt-agttgatcatctca-tgacatatcctgcatgtttagCATGGACAAGGAGTCCCAATAGCAGTAAGGCATATAGAATCAATGATACGGATGTCTGAAGCACATGCCAGAATGCACCTCAGACAGCATGTTACCCAGG
















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|208068431|gb|GD862277.1|GD862277
EST:     TGTCTATGCCGAACTGCGGAGGGAATCTTCA                         CACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
genomic: TGTCTATGCCGAACTGCGGAGGGAATCTTCAgtaataccct ... ccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
EST: gi|51335956|gb|CO979822.1|CO979822
EST:     ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCA                         CACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
genomic: ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCAgtaataccct ... ccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
EST: gi|193452513|gb|FK417533.1|FK417533
EST:     ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCA                         CACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
genomic: ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCAgtaataccct ... ccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
EST: gi|24136777|gb|BU927287.1|BU927287
EST:     ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCA                         CACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
genomic: ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCAgtaataccct ... ccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
EST: gi|193406876|gb|FK370963.1|FK370963
EST:     ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCA                         CACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
genomic: ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCAgtaataccct ... ccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
EST: gi|193447000|gb|FK413685.1|FK413685
EST:     ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCA                         CACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
genomic: ATATGGATAAACTGTCACATGTCTATGCCGAACTGCGGAGGGAATCTTCAgtaataccct ... ccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
EST: gi|208075385|gb|GD874272.1|GD874272
EST:     CGGAGGGAATCTTCA                         CACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG
genomic: CGGAGGGAATCTTCAgtaataccct ... ccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtagttattgtttgtattgaattcactaacaagctgctctaatttccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGGATGTCTGAAGCACATGCGAGAATGCATCTCAGGCAACATGTTACACAAG
                                          tttccttgt  CT-rich tract
              tattgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaataccctgtcataactttttttaccaaactagattgtagttattgtttgtattgaattcactaacaagctgctctaatttccttgtatagCACGGACAAGGAGTCCCTATTGCTGTAAGGCACATTGAATCAATGATAAGGATGTCTGAAGCACATGCGAGAATGCATCTCAGGCAACATGTTACACAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC