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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaacttgtttatgagtttcgtgagtgacttgagcaattttagttcatactactcttctttttagggtttaatagtgttcttattcattgcatatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATGGAAAGAGTTCTAGGGCCACTACCTCCCCATATGGTGGTCAGGGCCGA

Basic information

species Glycine max
transcript GLYMA03G33100.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 9
lower sequence: AT3G53570.2 (Arabidopsis thaliana), 3'ss of exon 10
aaacttgtttatgagtttcgtgagtgacttgagcaattttagttcatactactcttctttttagggtttaat-agtgttcttattcattgcatatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATGGAAAGAGTTCTAGGGCCACTACCTCCCCATATGGTGGTCAGGGCCGA
        | |  |  ||  ||  || | |         ||   ||  ||| || |||    | |  |  || |  ||| |   |   |  |     |||||||||||| ||||||||||| ||||| |||||||||||| | |||||||||||||| || ||||| ||  |||| || ||||||||| |||| |||||
-------gtgagtaactttatgtttg-catatcttccggtacaccaccctattcatctcaccatgtctccatcaacgttttctctggattaaaccttgcagGGAGAGGCGCTTTTCCAAACGCATGAAAACTTGGAACATTTGGCCATGATGGAAAGGGTCCTAGGACCTTTACCACCTCATATGGTGCTCAGAGCCGA

upper sequence: GLYMA03G33100.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv08s0040g02640.t01 (Vitis vinifera), 3'ss of exon 9
aaacttgtttatgagtttcgtgagtgact-tgagcaattttagttcatactactcttctttttagggtttaa--tagtgttcttattcattgcatatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATGGAAAGAGTTCTAGGGCCACTACCTCCCCATATGGTGGTCAGGGCCGA
 ||  ||  ||||||| |    | ||| | |  |   |||   ||| |   | | |  | ||| |  || |   ||   ||||| |   || |  |   |||||| ||||| ||||||||||||||||||||||||||||||||||| |||||||| || ||  | || || || || |  ||||||||| | || || ||
-aatatgactatgagtctgaatattgattgttggatgtttctattcttg--attgtgatgtttggatttgaggttatatttcttctcttttactcactggcagGGGGAGGCCCTTTTCCAAACACATGAGAACTTGGAACATCTTGCAATGATGGAGAGGGTGTTGGGACCTCTGCCCCAACATATGGTGCTGAGAGCTGA
















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|192302499|gb|FG994821.1|FG994821
EST:     ATCCTTGTGATCTTTGGAGTGTGGGCTGCATACTGGTTGAGCTTTGCTCT                         GGAGAGGCACTTTTCCAAACACATGAGAACTTGGAATATCTTGCCATGATG
genomic: ATCCTTGTGATCTTTGGAGTGTGGGCTGCATACTGGTTGAGCTTTGCTCTgtaagtaatt ... atatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATG
EST: gi|192305976|gb|FG996492.1|FG996492
EST:     ATCCTTGTGATCTTTGGAGTGTGGGCTGCATACTGGTTGAGCTTTGCTCT                         GGAGAGGCACTTTTCCAAACACATGAGAACTTGGGACATCTTGCCATGATG
genomic: ATCCTTGTGATCTTTGGAGTGTGGGCTGCATACTGGTTGAGCTTTGCTCTgtaagtaatt ... atatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATG
EST: gi|192302498|gb|FG994820.1|FG994820
EST:     ATCCTTGTGATCTTTGGAGTGTGGGCTGCATACTGGTTGAGCTTTGCTCT                         GGAGAGGCACTTTTCCAAACACATGAGAACTTGGAATATCTTGCCATGATG
genomic: ATCCTTGTGATCTTTGGAGTGTGGGCTGCATACTGGTTGAGCTTTGCTCTgtaagtaatt ... atatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atactactcttctttttagggtttaatagtgttcttattcattgcatatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATGGAAAGAGTTCTAGGGCCACTACCTCCCCATATGGTGGTCAGGGCCGA
                    gtttaat  putative branch site (score: 4)
         ttcttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaacttgtttatgagtttcgtgagtgacttgagcaattttagttcatactactcttctttttagggtttaatagtgttcttattcattgcatatgagcagGGAGAGGCACTTTTCCAAACACATGAGAACTTGGAACATCTTGCCATGATGGAAAGAGTTCTAGGGCCACTACCTCCCCATATGGTGGTCAGGGCCGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - tgagtga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agtgttc