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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGACCAAGAAGCCGGCTAAAGGAGCAGGGCGTGGCAAAGCTGCTGCTAAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcgcctcaaattctttggttcagtagtttccatggatacaacttttattgccgtacaaaagttttttcatctggttactgccaatcatttttt...

Basic information

species Arabidopsis thaliana
transcript AT1G20693.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G20693.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA06G01970.4 (Glycine max), 5'ss of exon 2
CTGTGACCAAGAAGCCGGCTAAAGGAGCAGGGCGTGGCAAAGCTGCTGCTAAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcg--cctcaaattctttggttcagt-agtttccatggatacaacttttattgccgtacaaaagttttttcatctggttactgccaatcatttttt
  |   ||   |    |||||    | | |   |          || || || ||||| ||||| |||||||||||  | |||||||||||||||||||||||||  |      || || | |  | | || |   |||||   |      ||| | || ||    || | |||| || ||     |||   | ||||| |  
AGGGAGCCGCCACCAAGGCTAGGAAACCCGCCGGCAAGGGGAAGGCAGCGAAAGACCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattattatatttctaactatacgatccattcgatttccgatgcgctctcttctctttccaccgaataattttatcgtcaaa--actttta-tcattgtcc

upper sequence: AT1G20693.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: GLYMA04G01840.8 (Glycine max), 5'ss of exon 3
---CTGTGACCAAGAAGCCGGCTAAAGGAGCAGGGCGTGGCAAAGCTGCTGCTAAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcct----cgcctcaaattctttggttcagtag-tttccatggatacaacttttattgccgtacaaaagttttttcatctggttactgccaatcatttttt
     |   |||  ||| |    |||   || ||    || || || ||    || || || ||||| |||||||||||  | |||||||||||||||||||||||||  |           |  |||  | |||| | |  ||||   |      ||| | || ||    || | |||| || ||     |||   |  | | |   
AGGGCGCCGCCACCAAGACTAGGAAACCCGCCGGAAAGGGGAAGGCAGCG---AAAGATCCTAACAAGCCAAAGAGGCCTCCAAGTGCTTTCTTCGTTTTCATgtaattataatatattgttatctctacgattcatttgacttccgatgcgctctcttatctttcctccgaataattttatcgtcaaa--acttttatccttgt---

upper sequence: AT1G20693.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv18s0122g01190.t01 (Vitis vinifera), 5'ss of exon 3
---CTGTGACCAAGAAGCCGGCTAAAGGAGCAGGGCGTGGCAAAGCTGCTGCTAAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcgcctcaaattctttggttcagtagtttccatggatacaacttttattgccgtacaaaagttttttcatctggttactgccaatcatttttt
   |||   | | |||| | |  ||   | ||  |   || |||||  | |  |||||||| ||||| || ||||||||||||||||| || |||||||||||||||        |    || |    || |  | | |  |   ||     ||  |||    |  |    ||| || |  |  ||| |   ||  |||    
GGGCTGCTGCTACGAAGGCAGGAAAGAAAACAAAGAA-GGAAAAGC--CAGTAAAGGACCCTAACAAGCCTAAGAGGCCAGCCAGTGCCTTTTTCGTTTTCATgtaaaatctcaatttttttttcctatttaaaaatctt-acaaattgtttttagattattatctac---tttatttactttattatt-ttaacgattgaag

upper sequence: AT1G20693.3 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv04s0044g00110.t01 (Vitis vinifera), 5'ss of exon 2
CTGTGACCAAGAAGCCGGCTAAAGGAGCAGGGCGTGGCA--AAGCTGCTGCTAAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaat---cctcgcctcaaattct--ttggttcagtagtttccatggatacaactttta--ttgccgtacaaaagttttttcatctggtta-ctgccaatcatttttt--------
    |     |  |||| |  ||  |  | |||   | |  |    ||||  ||||| || ||||| || |||||||| || ||||| ||||||||||||||||| |    |||||   |||   |     | || ||  |||   |   | | | |||||  ||        ||    || | || ||   | ||    ||| ||  ||        
--AAGGTGCCGCTGCCGTCGGAAAAAAGACGGCTAAGAAGGAGAAGGCTGTAAAGGATCCAAACAAGCCGAAGAGGCCTGCTAGTGCCTTCTTCGTTTTCATgtactgaatctcgctagaaacgttgaccagatctgtcattttt-tccttccgatttttaggttttttatttaatccattctgatgtgagaatctctttatccttcgttgaatgaag

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|163977800|gb|ES043825.1|ES043825
EST:     AGGACCCCTAACAAACCAAAGAGGCCAGCCGGTGCTTTCTTCGTTTTCAT                         GGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCC
genomic: AGGACCCC-AACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcg ... tgatgtgtagGGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCC
EST: gi|164068876|gb|ES124453.1|ES124453
EST:     AAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCAT                         GGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTC
genomic: AAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcg ... tgatgtgtagGGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTC
EST: gi|164158781|gb|ES187958.1|ES187958
EST:     CTTCGTTTTCAT                         GGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT
genomic: CTTCGTTTTCATgtaatcctcg ... tgatgtgtagGGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT
EST: gi|164067173|gb|ES061782.1|ES061782
EST:     AAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCAT                         GGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT
genomic: AAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcg ... tgatgtgtagGGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT
EST: gi|116400368|gb|EG442960.1|EG442960
EST:     AAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCAT                         GGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT
genomic: AAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcg ... tgatgtgtagGGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT
EST: gi|163975361|gb|ES019807.1|ES019807
EST:     CTTTC-TCGTTTTCAT                         GGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT
genomic: CTTTCTTCGTTTTCATgtaatcctcg ... tgatgtgtagGGAAGATTTCCGTGAGACTTTCAAGAAGGAAAACCCCAAGAACAAGTCTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTGACCAAGAAGCCGGCTAAAGGAGCAGGGCGTGGCAAAGCTGCTGCTAAGGACCCCAACAAACCAAAGAGGCCAGCCAGTGCTTTCTTCGTTTTCATgtaatcctcgcctcaaattctttggttcagtagtttccatggatacaacttttattgccgtacaaaagttttttcatctggttactgccaatcatttttt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG