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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttattcattgtctctatatcatttgagttttccaatatggattcatggttctttgttgtctttatctcatttgaatttattgtgttggactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTTGACATGGAACGAGATCTTCTTACGCCGACCTTCAAAAAGAAAAGGCCTC

Basic information

species Arabidopsis thaliana
transcript AT4G23850.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: LOC_Os01g46750.4 (Oryza sativa), 3'ss of exon 14
-----------gttattcattgtctctatatcat---------ttgagttttccaatatgg-attcatggttctttgttgtctttatctcatttgaatttattgtgttggactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTTGACATGGAACGAGATCTTCTTACGCCGACCTTCAAAAAGAAAAGGCCTC
            |||||  |||  | | | || |         || |  | | | ||||   |    ||     ||| |    ||| ||| ||  || ||  |  ||     ||||||| | ||||| || ||  |||| |||||  | |||||||| |||||||||||||||||||| || ||| |  |||| || || |  ||||||||  | ||||
gtaatattttgattattgcttgcttttttttcctgaaaggaaattaatctcttctatatatcacgtttgtccgcttgctcctattaactcctt--aactttctacgt--acttttgcagCTCAAAGGTTTTGAATTCATAAAGGCTGTACATCTTGAACCAGTGCCATTTGACATGGACCGTGATTTGATTACTCCAACATATAAAAAGAAGCGCCCTC

upper sequence: AT4G23850.1 (Arabidopsis thaliana), 3'ss of exon 17
lower sequence: GLYMA05G36910.1 (Glycine max), 3'ss of exon 17
--gttattcattgtctctatatcatttgagttttccaatatggattcatggttctttgttg--tctttatctcatttgaatttattgtgttggactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTTGACATGGAACGAGATCTTCTTACGCCGACCTTCAAAAAGAAAAGGCCTC
   |||||   |||   | |||  | ||    |    ||||  ||  ||   |   || ||   ||||||   ||    ||| || ||  |    ||  ||| ||||||| || ||| | || || ||  |||||||||||||||| ||||||||||||||||| | |||| | || || || || || ||||| || ||  
accttattatatgtgcttgtat-gtctgctggtatatatatatatatatatataaatgatgaagctttatgcgatcctgatt-atagtaatttgtttgtcagTTGAAAGGTTTTGAGTTTATTAAAGCTGTTCATCTTGACCCAGTTCCATTTGACATGGAACGTGGTCTTATGACTCCAACATTTAAGAAGAAGAGACCCG
















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|125073905|gb|EL138062.1|EL138062
EST:     CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGGCAAAGAGAAAAAG                         ATGAAAGGGTTCGAGATCA
genomic: CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAGgttattcatt ... gactttgcagATGAAAGGGTTCGAGATCA
EST: gi|125057403|gb|EL126615.1|EL126615
EST:     CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAG                         ATGAAAGGGTTCGAGA
genomic: CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAGgttattcatt ... gactttgcagATGAAAGGGTTCGAGA
EST: gi|124711162|gb|EH802564.1|EH802564
EST:     TCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAG                         ATGAAAGGGTTCGAGATCATCA
genomic: TCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAGgttattcatt ... gactttgcagATGAAAGGGTTCGAGATCATCA
EST: gi|116427901|gb|EG470493.1|EG470493
EST:     CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAG                         ATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTT
genomic: CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAGgttattcatt ... gactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTT
EST: gi|116458240|gb|EG500832.1|EG500832
EST:     CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAG                         ATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTT
genomic: CAAAGGAATTCATTCTCGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAGgttattcatt ... gactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTT
EST: gi|125226862|gb|EL240947.1|EL240947
EST:     CGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAG                         ATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTT
genomic: CGGAGAACTTGTTAAAATGGCCAAAGAGAAAAAGgttattcatt ... gactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcatggttctttgttgtctttatctcatttgaatttattgtgttggactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTTGACATGGAACGAGATCTTCTTACGCCGACCTTCAAAAAGAAAAGGCCTC
                  tttatctcatttgaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttattcattgtctctatatcatttgagttttccaatatggattcatggttctttgttgtctttatctcatttgaatttattgtgttggactttgcagATGAAAGGGTTCGAGATCATCAAGGCGATTCATCTTGACCCAGTGCCATTTGACATGGAACGAGATCTTCTTACGCCGACCTTCAAAAAGAAAAGGCCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA