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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttgtttgtcattaatggtgtgttgtatgtatcctgctagttcccattgattaagttgattgaacattctgtccaattcatgctgtgattattttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTATTTCATATTGCATACCCTAGCGCACCAGAAACATCAAAGACAGAGTTGA

Basic information

species Glycine max
transcript GLYMA10G42250.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G42250.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv01s0011g03280.t01 (Vitis vinifera), 3'ss of exon 1
------ttgtttgtcattaatggtgtgttgtatgtatcctgctagttcccattgattaagttgattgaacattctgtccaattcatgctgtgattattttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTATTTCATATTGCATACCCTAGCGCACCAGAAACATCAAAGACAGAGTTGA
| ||| | || | |||||| || | ||||| |||| | | | ||| | || || | | |||| | | ||| || | |||||||| ||||| | ||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| || || ||||| | | ||||| ||||||
gcatattcatttacctata-taatgtgttaggggtttttgtgtagttaatattg-tcgtttcgcctgatc-ttttgacta--tcat-ttattattcttgtattcagAGACTGGCATCTGGTGAATGGTTTACTGCTCGAGTTTCTGCATGTGGACTGTTTCATATTGCTTACCCAAGTGCCCCAGAGATGTTAAAGATGGAGTTGC
















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|254336134|gb|GR841459.1|GR841459
EST:     TCAAATGAGGGAGAGTGATTTGGGTTGAATATTACATCCCGTTGGTGAAG                         AGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTA
genomic: TCAAATGAGGGAGAGTGATTTGG-TTGAATATTACATCCCGTTGGTGAAGgtcagctaac ... ttttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTA
EST: gi|209719391|gb|BW674471.1|BW674471
EST:     CTCAAATGAGGGAGAGTGATTTGGTTGAATATTACATCCCGTTGGTGAAG                         AGATTGGCAGCANGTGAATGGTTTACTGCTCGAGTCTCTGCATGT
genomic: CTCAAATGAGGGAGAGTGATTTGGTTGAATATTACATCCCGTTGGTGAAGgtcagctaac ... ttttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGT
EST: gi|254343717|gb|GR857473.1|GR857473
EST:     CTCAAATGAGGGAGAGTGATTTGGTTGAATATTACATCCCGTTGGTGAAG                         AGATTGGCAGCAG-TGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTA
genomic: CTCAAATGAGGGAGAGTGATTTGGTTGAATATTACATCCCGTTGGTGAAGgtcagctaac ... ttttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTA
EST: gi|23725947|gb|BU760948.1|BU760948
EST:     CTCAAATGAGGGAGAGTGATTTGGTTGAATATTACATCCCGTTGGTGAAG                         AGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTA
genomic: CTCAAATGAGGGAGAGTGATTTGGTTGAATATTACATCCCGTTGGTGAAGgtcagctaac ... ttttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattaagttgattgaacattctgtccaattcatgctgtgattattttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTATTTCATATTGCATACCCTAGCGCACCAGAAACATCAAAGACAGAGTTGA
                                             ttttgttc  CT-rich tract
 attattttgtt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttgtttgtcattaatggtgtgttgtatgtatcctgctagttcccattgattaagttgattgaacattctgtccaattcatgctgtgattattttgttcagAGATTGGCAGCAGGTGAATGGTTTACTGCTCGAGTCTCTGCATGTGGACTATTTCATATTGCATACCCTAGCGCACCAGAAACATCAAAGACAGAGTTGA

-tgtttgt
- - - - - - - tggtgtg
- - - - - - - - - - - tgtatgt
- - - - - - - - - - - - - - - tcctgct
- - - - - - - - - - - - - - - - - - - - -cccattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatgct