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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgacatcattagcttttctaaggttgagtatattaatttttaaaaatatatattacattgcatgtttcctcatttgtcttttttacccctaatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTGCATTGCTAAAACCTCATGATAGAATCATGGGACTTGATCTACCACATGG

Basic information

species Glycine max
transcript GLYMA09G33480.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 5
-atgacatcattagcttttctaaggttgagtatattaatttttaaaaatatatattacattgcatgtttcctcatttgtcttttttacccctaatt-tgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTGCATTGCTAAAACCTCATGATAGAATCATGGGACTTGATCTACCACATGG
   | |    |    || |||     |   |   ||  |||||   |  |  || ||   ||   | ||    |  ||| ||  | |||| |  || |||||||||||||||| || | ||||| ||  |||| ||||||||||||||||||||| |  ||||| ||||||| ||||| |||| ||||||||| || |||||
ccaggcgctgt-gttttctcttcttctttctcctttcctttttttcagcaggtaatagtgtgtcagctttgataaatgt-ttaatcacccttggttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAAGCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG

upper sequence: GLYMA09G33480.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0211g00100.t01 (Vitis vinifera), 3'ss of exon 5
--atgacatcattagcttttctaaggttgagtatattaatttttaaaaatatatattacattgcatgtttcctcatttgtcttttttacccctaatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTGCATTGCTAAAACCTCATGATAGAATCATGGGACTTGATCTACCACATGG
   ||   ||  |   | ||||    ||   |   ||  |||||   |  || || ||   ||   | ||    |  ||| |  |   ||  |  | |||||||||||||||| || | ||||| ||  |||| ||||||||||||||||||||| |  ||||||||||||| ||||| |||| ||||||||| || |||||
ctgtgttttctcttcttcttctttcttt--ctcctttcctttttttcagcatgtaatagtgtgtcagctttgataaatgtttaatcaccctttgttatgcagTGAACGTGCAGTCTTTATCTGGCTCGCCTGCAAATTTTCAAGTTTACACTGCACTATTAAAACCTCATGAAAGAATTATGGCACTTGATCTTCCTCATGG
















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|207692648|gb|GD674873.1|GD674873
EST:     ACAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: -CAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193445566|gb|FK412657.1|FK412657
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|207700103|gb|GD683084.1|GD683084
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193438324|gb|FK400033.1|FK400033
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|207839851|gb|GD810044.1|GD810044
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGGACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193392902|gb|FK359678.1|FK359678
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193712073|gb|FK648816.1|FK648816
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|208217137|gb|GE008617.1|GE008617
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193588700|gb|FK540098.1|FK540098
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCT
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCT
EST: gi|193408671|gb|FK374173.1|FK374173
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|208083475|gb|GD883985.1|GD883985
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCACTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|208046332|gb|GD847250.1|GD847250
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193367587|gb|FK332049.1|FK332049
EST:     CAAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: C-AAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|208025377|gb|GD823425.1|GD823425
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|207779220|gb|GD750750.1|GD750750
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|208209401|gb|GE003853.1|GE003853
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193633479|gb|FK579649.1|FK579649
EST:     TC-AAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193494239|gb|FK459263.1|FK459263
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCAGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCCTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|207789798|gb|GD759479.1|GD759479
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|208083643|gb|GD884027.1|GD884027
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAAT-GGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|193308001|gb|FK272023.1|FK272023
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCT
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCT
EST: gi|208220568|gb|GE017144.1|GE017144
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
EST: gi|208239465|gb|GE041337.1|GE041337
EST:     TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAG                         TGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG
genomic: TCAAAAACGTGCCTTGGAAGCATTTCGGTTGGATCCGGCTAAATGGGGAGgtaaaaaaga ... taatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aatatatattacattgcatgtttcctcatttgtcttttttacccctaatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTGCATTGCTAAAACCTCATGATAGAATCATGGGACTTGATCTACCACATGG
                                          ccctaat  putative branch site (score: 3)
                  tgtttcctcatttgtc  CT-rich tract
                           atttgtctttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgacatcattagcttttctaaggttgagtatattaatttttaaaaatatatattacattgcatgtttcctcatttgtcttttttacccctaatttgcagTGAACGTGCAGCCTCTGTCTGGTTCTTCTGCCAATTTTCAAGTTTACACTGCATTGCTAAAACCTCATGATAGAATCATGGGACTTGATCTACCACATGG

-tgacatc
- - - - - - - - - - - ggttgag
- - - - - - - - - - - - - - - - - - - - - aaaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cattgca