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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgttttatgggagcaagatgagaatgcagttatatatgtttattgtctctattatatggtgcaaaacttacatgttctctttctccataattctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGAAATTATCCTACCTTCGTCTGCCCAAATATTGCTCGGAGATCACTGGATA

Basic information

species Glycine max
transcript GLYMA03G25740.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G25740.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv12s0028g03370.t01 (Vitis vinifera), 3'ss of exon 11
ttgttttatgggagcaagatgagaatgcagttatatatgtttattgtc--tcta-ttata-----tggtgcaaaactta--catgttctctttctccataatt------ctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGAAATTATCCTACCTTCGTCTGCCCAAATATTGCTCGGA-GATCACTGGATA-
                  ||||     |  || |||||  || ||||   |||| |||||     ||| |  ||  |||  | |  |||  ||  |||   ||      |||||||||||||||||| || |||||  | |||||||||||| | |||||  |||  || ||   |   ||   |  |       |||   ||| |||   |  ||| 
----------------ccatgatttccctattttatatagttcttgttaatctaattataaaaactggagacaagattatccctaatcttctttgccactgtttcctttctttcagATGGTGGATGCTTTCATGGCAGTGAGACCACTTCCCAATATGTTCAACTAGAAATAG--TGATTTGAACAACTTTCGATTTGTGGGGATGATTGTTTCATAA
















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|207776825|gb|GD747795.1|GD747795
EST:     CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAG                         ATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGA
genomic: CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAGgtacacattc ... attctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGA
EST: gi|17964097|gb|BM270837.1|BM270837
EST:     CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAG                         ATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGA
genomic: CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAGgtacacattc ... attctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGA
EST: gi|18039483|gb|BM307777.1|BM307777
EST:     CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAG                         ATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGAC
genomic: CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAGgtacacattc ... attctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGAC
EST: gi|15201309|gb|BI424804.1|BI424804
EST:     CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAG                         ATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGA
genomic: CTGAACTAGTGGAGAGGCATCGCAGAGCTCGGGCTTCTGTGACTGAAGAGgtacacattc ... attctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtctctattatatggtgcaaaacttacatgttctctttctccataattctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGAAATTATCCTACCTTCGTCTGCCCAAATATTGCTCGGAGATCACTGGATA
                    aacttac  putative branch site (score: 2)
                              ttctctttctccataa  putative PPT
                                          ataattcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgttttatgggagcaagatgagaatgcagttatatatgtttattgtctctattatatggtgcaaaacttacatgttctctttctccataattctttcagATGGTGGATGCATTTATGGCTATCAGACCACTTCCCCACATGTTTGACTGAAATTATCCTACCTTCGTCTGCCCAAATATTGCTCGGAGATCACTGGATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - gaatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgca