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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctactctccaaaccactttacgaatgttcttcacctacaatgtaatccaatagttaatccttaaatttcctggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA

Basic information

species Arabidopsis thaliana
transcript AT2G26330.1
intron # 24
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
-------------gtctactctccaaaccactttacgaatgttcttc--acctacaatgtaatccaatagttaatccttaaatttcct--ggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA
              | || | |  |    | ||||  |   |||| |  |  || | |  | |  |  ||||| |   |  ||   ||  | |     |||| | ||  ||  | || ||||| || || ||||||||||| |||||||| || || || || ||||||||||| ||||| || || ||||||||||||||
tttgtagtgtttcatttattata-atggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA

upper sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA04G05910.1 (Glycine max), 3'ss of exon 16
gtctactctccaaaccactttacgaatgttcttcacctacaatgtaatccaatagttaatccttaaatttcctggtga--catcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA
             ||    |    | ||| | | |   | | || |  |    |  |  |  ||    || || |  |    ||||| | ||| ||  | || ||||| || || ||||| ||||| |||||||| || || || || ||||||||||| ||||| || || ||||||||||||||
-----------gtactttatcttaactgtacct-attgaaactgaagactgtaacatgctgattgttcttgcttgaaaattgtcagTTAATTACTCACCTCCAAAGCTAGTGATTCTTCACATGAATATGGCACTTCATGTGTATGATGATATCATGAGGATGACCGAAAACCTAAGTGAGAAGTA

upper sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: GLYMA17G34380.2 (Glycine max), 3'ss of exon 23
---------gtctactctccaaaccactttacgaatgttcttc-acctac---aatgtaatccaata-gttaatccttaaatttcct--ggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA
          | || | |   |   | | ||    | |  |||  ||||    ||  |||    | | |||| |   |  ||   ||  | |     |||| | ||  ||  | || ||||| || || ||||||||||| |||||||| || || || || ||||||||||| ||||| || || || |||||||||||
tgccggattttgtagtgtttgatatattataatggtatcattctgcctattgaaacttaagttgacaagttactgactgcataagctatgctattgacagTTAATTTCTCCCCCCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTGAGTGAGAAGTA

upper sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
------------------gtctactctccaaaccactttacgaatgttcttcacctacaatgtaatccaatagttaatcctta-aatttcctggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA
                   | || | |  |||     |||| | | | | |     | | |    ||||     |||    |  | ||| ||    ||| |||| || || || ||||||||||| || |||||||| ||||| |||||||| || || ||||||||||||||||||||||| || ||  | |||||||||||
ttatatctgtatcccttaatatattttgaaaaatgtgttactattttccctt-ttgaaacttctctccatctactaactaatgtagtttgctaa--acaacagTTACATACTCAACACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTA

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|164124476|gb|ES113455.1|ES113455
EST:     CCGACCGCATAATCCTCCTCCTTTTCTTGATGGATCACTTGACAAACCAG                         TAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACA
genomic: CCGACCGCATAATCCTCCTCCTTTTCTTGATGGATCACTTGACAAACCAGgtctactctc ... gtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACA
EST: gi|164077283|gb|ES208443.1|ES208443
EST:     GATGGATCACTTGACAAACCAG                         TAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCC
genomic: GATGGATCACTTGACAAACCAGgtctactctc ... gtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCC
EST: gi|164196805|gb|ES051575.1|ES051575
EST:     TCACTTGACAAACCAG                         TAACTTATTC-ACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCC
genomic: TCACTTGACAAACCAGgtctactctc ... gtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttcacctacaatgtaatccaatagttaatccttaaatttcctggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA
                        agttaat  putative branch site (score: 4)
                          ttaatccttaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctactctccaaaccactttacgaatgttcttcacctacaatgtaatccaatagttaatccttaaatttcctggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT