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

gtgagtattggatatgagagggatatttttttaaaagattttatttatttttaatcaaattttcatatgcctctcttatttcaagtgcagGTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTTAGAGCCTAATAAAGGGTTGACATGGCAAATGACAAAAAGAAGAGGTGAT

Basic information

species Glycine max
transcript GLYMA18G01710.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv00s0187g00030.t01 (Vitis vinifera), 3'ss of exon 4
gtgagtattggatatgagagggatatttttttaaaagattttatttatttttaatcaaattttcatatgcctctcttatttcaagtgcagGTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTTAGAGCCTAATAAAGGGTTGACATGGCAAATGACAAAAAGAAGAGGTGAT
|||||| ||||| || |     |||| ||||| |  |  ||| |    ||| | || |     | |||| |  |    || ||| | ||| || |||| ||| ||||||||  |||| |||||||||||||| ||||| ||||| |||||||||||||| |||||||| |||||||||||||||||||||
gtgagtgttggacataa-----atatcttttttatggcatttgt---gtttcagtctacccaacttatgtcatt----ttccaattccagATATATAAGACTAGTGAGGAAATATGGCTTGGAGATTTCACAACCTGGTTTAGAACCTAATAAAGGGTTAACATGGCAGATGACAAAAAGAAGAGGTGAT

upper sequence: GLYMA18G01710.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv01s0137g00770.t01 (Vitis vinifera), 3'ss of exon 8
gtgagtattggatatgagagggatatttttttaaaagattttatttatttttaatcaaattttcatatgcctctcttatttcaagtgcagGTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTTAGAGCCTAATAAAGGGTTGACATGGCAAATGACAAAAAGAAGAGGTGAT
|||||| ||||| || |     |||| ||||| |  |  ||| |    ||| | || |     | |||| |  |    || ||| | ||| || |||| ||| ||||||||  |||| |||||||||||||| ||||| ||||| |||||||||||||| |||||||| |||||||| ||||||||||||
gtgagtgttggacataa-----atatcttttttatggcatttgt---gtttcagtctacccaacttatgtcatt----ttccaattccagATATATAAGACTAGTGAGGAAATATGGCTTGGAGATTTCACAACCTGGTTTAGAACCTAATAAAGGGTTAACATGGCAGATGACAAAGAGAAGAGGTGAT
















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|15661819|gb|BI699190.1|BI699190
EST:     ATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAAGA                         GTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTT
genomic: ATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAAGAgtgagtattg ... tcaagtgcagGTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTT
EST: gi|192319061|gb|FK010625.1|FK010625
EST:     ATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAAGA                         GTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTT
genomic: ATATTCATATGGGATGAAGACCTGGGTGTTGAGCATTTTAATGCGGAAGAgtgagtattg ... tcaagtgcagGTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agattttatttatttttaatcaaattttcatatgcctctcttatttcaagtgcagGTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTTAGAGCCTAATAAAGGGTTGACATGGCAAATGACAAAAAGAAGAGGTGAT
             ttttaat  putative branch site (score: 3)
                                tgcctctcttatttc  putative PPT
     ttatttatttttaatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtattggatatgagagggatatttttttaaaagattttatttatttttaatcaaattttcatatgcctctcttatttcaagtgcagGTACATAAAACTGGTGAGGAAGCATGGGTTGGAGATTTCACAGCCTGGCTTAGAGCCTAATAAAGGGTTGACATGGCAAATGACAAAAAGAAGAGGTGAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG