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'   		27  
 5'  3'   		28  
 5'  3'   		29  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatctgaattttcttttggtatcctgtacttgtgcctgtgacttgcaagtgttgtatttgatgattgtttttatatgttttgaaacttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCTGTGAAGTACTCCATAGTTGAGCGTCCAGAGAAGATAGATGAGATCATAT

Basic information

species Glycine max
transcript GLYMA07G40230.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA07G40230.2 (Glycine max), 3'ss of exon 24
lower sequence: Vv12s0035g01840.t01 (Vitis vinifera), 3'ss of exon 24
gtatctg---aattttcttttggtatcctgt-acttgt--gcctgtgacttgcaagtgttgtatttgatgattgtttttatatgtt------ttgaaacttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCTGTGAAGTACTCCATAGTTGAGCGTCCAGAGAAGATAGATGAGATCATAT
||||||    ||      || | |||||| | |||| |     |  |  ||| | |   | || ||     |||||   |||  ||      || |   ||||||||||  | | | |||| ||||||||||| ||| |||| || || |||||||| || || || || ||||||||||| |||||||| ||||||||||||||||
gtatctacaaaacaggaattggatatccttttacttcttaagttacggtttgaagggcatctagttaccatttgttggcataacttcattgtttcatgtttctatagGTGCGGACAGCCAGTCCAGCTGCATTCACTAGAGCAACAGTCGTCATTGCCGTAAAATATTCTATAGTTGAGCGGCCAGAGAAAATAGATGAGATCATAT
















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|208161149|gb|GD960943.1|GD960943
EST:     TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAG                         GTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT
genomic: TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAGgtatctgaat ... acttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT
EST: gi|208298167|gb|GE091058.1|GE091058
EST:     TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAG                         GTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT
genomic: TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAGgtatctgaat ... acttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT
EST: gi|13789058|gb|BG651649.1|BG651649
EST:     TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAG                         GTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT
genomic: TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAGgtatctgaat ... acttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT
EST: gi|151410822|gb|EV280637.1|EV280637
EST:     TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAG                         GTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT
genomic: TGGGCAAAATTGCTCTTATTGAGCCTGTTAAACTCATCCCTGCACTCAAGgtatctgaat ... acttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttgcaagtgttgtatttgatgattgtttttatatgttttgaaacttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCTGTGAAGTACTCCATAGTTGAGCGTCCAGAGAAGATAGATGAGATCATAT
                atttgat  putative branch site (score: 5)
                                              cttctat  putative PPT
               tatttgatgattgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatctgaattttcttttggtatcctgtacttgtgcctgtgacttgcaagtgttgtatttgatgattgtttttatatgttttgaaacttctatagGTAAGAAGAACCAGCCCAGCTGCATTTACTCGAGCTACTGTTGTCATTGCTGTGAAGTACTCCATAGTTGAGCGTCCAGAGAAGATAGATGAGATCATAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA