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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgatctatgtgctgactttggggcctggtattggaaattatgattagttagccaatcattttcttgactttatgtatttgtgtttttgtttcactacagGTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG

Basic information

species Glycine max
transcript GLYMA03G03120.1
intron # 18
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g51430.2 (Oryza sativa), 3'ss of exon 16
------ttgatctatgtgctgactttggggcctggtattggaaattatgattagttagccaatcattttcttgactttatgtatttgtgtttttgtttcactacagGTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG
       | |   ||||| |   | ||  |  ||   || | | |||     | |||  || |      ||   |       |      ||| |||||   ||||||||||||||||||||||||| || |||||||||||||| || |||
acataggttaaagatgtgttt-ttctgcagtttgtcctttgcagttaca--cacttaagcattttaaagctcttcacggcaaagcaaaatttctgttt---tacagGTTAATTTTGAAGATACCTGCAAAGGATTTCTTGAGGTTGCCAAG

upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G070045_T01 (Zea mays), 3'ss of exon 12
ttgatctatgtgctgactttggg-gcctggtattggaaattatgattagttagccaatcattttcttgactttatgtatttgtgtttttgtttcactacagGTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG
   || | |    |||  ||    |     |  || | |   |   ||  |   || |||  || |    |||      |        | ||    ||||||||||||||||||| ||||| || |||||||||||||| || |||
-ctatttgtagcttgatgttaattgttctttgctgtacaacgtttctatctcttcactcaccttatgccttttgaagtataaccaaaatattctgttacagGTTAATTTTGAAGACACCTGCAAAGGATTTCTTGAGGTTGCCAAG

upper sequence: GLYMA03G03120.1 (Glycine max), 3'ss of exon 18
lower sequence: EFJ12004 (Selaginella moellendorffii), 3'ss of exon 16
ttgatctatgtgctgactttggggcctggtattggaaattatgattagttagccaatcattttcttgactttatgtatttgtgtttttgtttcactacagGTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG
                                                       |  | |   |  |  ||  |  ||       || |  ||   ||||| ||||||||||| |||||||| || ||||||||||| || |||
-----------------------------------------------------gtacaagtccatctatcttccgctttctctcagttttaccatgtcagGTCAATTTTGAAGACACCTGTAAAGGGTTTCTTGAGGTGGCCAAG

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|14990484|gb|BI316157.1|BI316157
EST:     AGCTAAGTAATAGCACCATAGAAGCCCTTCCACAGAACTACGCTGAGCAG                         GTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG
genomic: AGCTAAGTAATAGCACCATAGAAGCCCTTCCACAGAACTACGCTGAGCAGgtttgttgtt ... ttcactacagGTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttagccaatcattttcttgactttatgtatttgtgtttttgtttcactacagGTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG
                 tcttgac  putative branch site (score: 3)
                                      tttttgtttc  putative PPT
                        tttatgtattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgatctatgtgctgactttggggcctggtattggaaattatgattagttagccaatcattttcttgactttatgtatttgtgtttttgtttcactacagGTTAATTTTGAAGATACCTGTAAGGGATTTCTTGAGGTAGCTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA