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

...tcagataattgcattttgacctgagttaatgatcattaatgctgttttgaaattctacttttccattacttttcttgattagttattcctctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGCAAAGATCAGATAGCCCTTTCTCCTTTCCTCGCCAAAAACGTTCAGTAAG

Basic information

species Glycine max
transcript GLYMA12G07590.1
intron # 16
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA12G07590.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv06s0004g03180.t01 (Vitis vinifera), 3'ss of exon 15
tcagataattgcattttgacctgagttaatgatcattaatgctgttttgaaattctacttttccattactttt---cttgattag--ttattcctctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAG---GCAAAGATCAGATAGCCCTTTCTCCTTTCCTCGCCAAAAACGTTCAGTAAG
   |    || |  |     | | |  |  |   ||     || ||||| |    |  |||||   | ||| |     || | ||  | |||  |  | ||||||||||||| || ||||| |||||||||| ||||||||||| | |||| ||   |||| |||||||||||||||| || || ||||||||   ||| || ||   
---gtaggttactctgcaggcagtgaaaggggcaatc--ctctcttttgcatacttttttttcatgttcttctaaatgtggtgaggctgattttttctcatgcagCTTCTTTGCTTCTTGGTATGAATGATGGTAGATCTGACAAGACAAGTAGCAGGCAACGATCAGATAGCCCTTTTTCGTTCCCTCGCCAGCGACGCTCTGT---
















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|208290053|gb|GE087115.1|GE087115
EST:     ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTG                         CTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
genomic: ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTGgtttgttgct ... ctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
EST: gi|254334594|gb|GR844379.1|GR844379
EST:     AATACTTTGGATGATACTG                         CTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
genomic: AATACTTTGGATGATACTGgtttgttgct ... ctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
EST: gi|16348338|gb|BI973933.1|BI973933
EST:     ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTG                         CTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
genomic: ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTGgtttgttgct ... ctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
EST: gi|16995876|gb|BM085248.1|BM085248
EST:     ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTG                         CTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
genomic: ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTGgtttgttgct ... ctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
EST: gi|10234250|gb|BE803138.1|BE803138
EST:     ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTG                         CTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
genomic: ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTGgtttgttgct ... ctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
EST: gi|19346695|gb|BM891575.1|BM891575
EST:     ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTG                         CTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC
genomic: ACATCAAATCCCAACCAGAGAAGGTGCCACGAATACTTTGGATGATACTGgtttgttgct ... ctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgaaattctacttttccattacttttcttgattagttattcctctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGCAAAGATCAGATAGCCCTTTCTCCTTTCCTCGCCAAAAACGTTCAGTAAG
                           tcttgat  putative branch site (score: 4)
                                     ttattcctctttat  putative PPT
                                attagttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcagataattgcattttgacctgagttaatgatcattaatgctgttttgaaattctacttttccattacttttcttgattagttattcctctttatgcagCTTCTTTACTCCTTGGGATGAATGATGTTAGATCTGACAGGGCAAGAAGGCAAAGATCAGATAGCCCTTTCTCCTTTCCTCGCCAAAAACGTTCAGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - -tgcattt
- - - - - - - - tgacctg
- - - - - - - - - - - - - - - - - - - -tgctgtt