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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaaagaaaaagaagcaaaatttgaaccaaaatgttttagatttatgtataatctttcacgtcattcatttgttgtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGA

Basic information

species Arabidopsis thaliana
transcript AT4G37930.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os03g52840.2 (Oryza sativa), 3'ss of exon 9
-----------------gtaaaaaagaaaaagaagcaaaa----tttgaaccaaaatgttttagatttatg----tataatctttcacgtcattcatttgtt-----gtcttgaa------agGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGA
                   || |   | | || |||  |     || | ||       | |      | ||    | | | |||  |    ||  |  ||         | |  |      ||||| ||||||| ||||| |||||||||||    ||||||||||| ||||| |||||||| ||||| || || || || || ||  ||||||||||  | |
gtatatacttgagcagaacaatagcaagatagtagcgtagggtgttggtactgtttcttctccatcctgtgactctgtgagcttcaaaaaaataaaaatgcctaatgaccctctaccgtctagGTTATGTATGACTTTGAGGACAAGATCAATGCTGCTGTCTTCCCAGGTCTGCAAGGTGGACCACATAATCATACCATTACTGGCTTAGCTGTTGCGCTTA

upper sequence: AT4G37930.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
---------------gtaaaaaagaaaaagaagcaaaatttgaaccaaaatgttttagatttatgtataatctttcacgtcattcatttgttgtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGA
                   | || |||||  ||||    |||||||      | ||  ||| |     ||   || | || ||  | ||  | |  | | ||||| ||||||||||||| ||||| |||||    |||||||| |||||||| |||||||| || || ||||| || || || ||  | ||||||||  | |
gtatggcatgatgaaaacgataaaaaaaactagcaggtgttgaacctg--cttcttgcattaaaaaccaaaggttta-gtgatatacttaatattct-atagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
















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|124729407|gb|EH820809.1|EH820809
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAG
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAG
EST: gi|125161978|gb|EL188868.1|EL188868
EST:     ATTTTCTTTCAGAAAGGGTGTTAAGGAAATTAAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: ATTTTC-TTCAGAAAGGGTGTTAAGGAAATT-AACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|124867423|gb|EH951860.1|EH951860
EST:     AAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: AAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|152033809|gb|BP816571.2|BP816571
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGA
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGA
EST: gi|124717404|gb|EH808806.1|EH808806
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGT
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGT
EST: gi|124869000|gb|EH953437.1|EH953437
EST:     CAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: CAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|152034927|gb|BP840236.2|BP840236
EST:     TTTTCTTCAGCAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: TTTTCTTCAG-AAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|125097008|gb|EL153611.1|EL153611
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGA
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGA
EST: gi|164222769|gb|ES035888.1|ES035888
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTC
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTC
EST: gi|124923059|gb|EL001289.1|EL001289
EST:     GGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATTGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCT
genomic: GGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTA-TGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCT
EST: gi|124880068|gb|EH958970.1|EH958970
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|125054211|gb|EL125020.1|EL125020
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         G-TTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|116443767|gb|EG486359.1|EG486359
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTGGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|125003036|gb|EL075305.1|EL075305
EST:     TGATTTTCTTCAGAAAGGGTGTTAAG-AAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTAGAAGACAAGATCAACCAAGCTGTCTT
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTT-GAAGACAAGATCAACCAAGCTGTCTT
EST: gi|124952671|gb|EL027923.1|EL027923
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTAGAAGACAAGATCAACCAAGCTGTCTTCCC
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTT-GAAGACAAGATCAACCAAGCTGTCTTCCC
EST: gi|125140494|gb|EL178729.1|EL178729
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|124716464|gb|EH807866.1|EH807866
EST:     TAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: TAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|125297760|gb|EL311845.1|EL311845
EST:     TTAACAAGCAAGGGAAAGAG                         GTTTCGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: TTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|125317334|gb|EL331419.1|EL331419
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTT-GTATGATTT-GAAGACAAGATCA
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCA
EST: gi|163992611|gb|ES126830.1|ES126830
EST:     GAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: GAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
EST: gi|125097545|gb|EL153974.1|EL153974
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAG
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAG
EST: gi|124968516|gb|EL042468.1|EL042468
EST:     TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAG
genomic: TGATTTTCTTCAGAAAGGGTGTTAAGGAAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAG
EST: gi|124836898|gb|EH921337.1|EH921337
EST:     AAATTAACAAGCAAGGGAAAGAG                         GTTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCT
genomic: AAATTAACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagG-TTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCT
EST: gi|124907012|gb|EH981092.1|EH981092
EST:     ACAAGCAAGGGAAAGAG                         GTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT
genomic: ACAAGCAAGGGAAAGAGgtaaaaaaga ... gtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaatgttttagatttatgtataatctttcacgtcattcatttgttgtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGA
                                           ttgtctt  CT-rich tract
     ttttagatttatgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaaagaaaaagaagcaaaatttgaaccaaaatgttttagatttatgtataatctttcacgtcattcatttgttgtcttgaaagGTTTTGTATGATTTTGAAGACAAGATCAACCAAGCTGTCTTCCCTGGTCTTCAAGGTGGTCCACACAACCACACTATCACAGGACTAGCTGTTGCTTTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT