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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtatacattgaagcgattcatttatagcatcaaccatatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG

Basic information

species Arabidopsis thaliana
transcript AT1G06390.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os01g10840.1 (Oryza sativa), 3'ss of exon 9
---------------------------------gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtat--------acattgaagcgattcatttatagc-------atcaaccatatactgtacccttg---acctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
                                   |   ||| | || |   |  | | || | || | | |  |||   ||  || ||   | |        | ||  ||   ||  || |  |||        | | |||| |  ||| |  | |   ||| |||| |||| || ||  | |||||||||||||| ||||||||||| || || ||||| ||||||||||||||||||||||||||||| 
gtagccatgttttcttatattggatcaccttcctcataccattttacttgcagggcattgt-aggccacttcaaaaccagtt-tctgcatcatgtttaatttgaaataaaaaaaatgtatctgcagctgcttaactgatccatctgttgttctttcgcttaccaccagATTTTCCACAAGAGAATGCCTCCAGAAGCCATAGACCTTGCTTCCCGTCTTCTCCAATATTCACCAAGTCTACGCTGCACTGCT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os05g11730.1 (Oryza sativa), 3'ss of exon 9
------------------------------gtagttcatctcaccttttg----ttcctggttaagca-------attactgaactcattacctaca---------------cag-----tatacattgaagcg-attcatttatagcatcaaccatatactg-tacccttgacctcc----agGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
                               ||  |||  ||| |||||     |||||||  ||  |        |  |||  |||||| || | |               |||     | |||| || |  | ||  ||    ||   ||  ||  ||||| |     | || ||     ||||||| || ||  |||||||||| |||||||||||||| || || || ||||||||||||||||| ||||| ||||||||||| 
gtaagcatacaatcttatccatgttgagtcatatatcacgtcatcttttatagtttcctggacaactatgaaaatgtagctgggctcatttccaataatagattctggacaccagatagctttacaatgcaatgtataaataaggaggtgcatacaggtactgatttttctaacttctgcgtagGTTTTCCACAAGAGGATGCCTCCTGAAGCAATAGACCTCGCTTCACGCCTTCTTCAATATTCACCGAGTCTCCGCTGCACTGCT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G045330_T02 (Zea mays), 3'ss of exon 9
---------------------------------------------------------------------------gtagttcatctcaccttttgttcctg------gttaagcaattactgaactcattacctacacagtatacattga-agcgattcatttatagcatcaaccatatactgtac-ccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
                                                                           ||||| ||     |    ||||          | | |  || |  |   |  || |  |  | | | |    | | |  |  ||| |||     | |  | | |||| | |   ||  ||||||| |||| || ||  | |||||||| ||||| ||||||||||| ||||| || ||||| |||||||||||||| |||||| |||| 
gtattcatatgttaaatcatgtttctgttcacatctattatccattttacctgcaggtactgtagttgtatacttgtagtccacagtccaaaatgttttcaaagggcgctgaagaacttgtttgcagatcatatcgaaactttgagctcagaatgcatcaattactaactgatgcctctactttccgttttatcctccagATTTTCCACAAGAGAATGCCTCCTGAAGCCATAGACCTTGCTTCTCGTCTCCTTCAGTATTCACCAAGTCTTCGCTGCTCTGCT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA06G42840.1 (Glycine max), 3'ss of exon 9
gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtatacattgaagcgattcatttatagcatcaaccatatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
    |  | |  ||    |   ||| || ||| ||      | |||| |   |    | ||  |||||  || | | | | ||    | |    ||| || ||   ||      |||||||| || || || |||||||| |||||||| |||||||||||  ||||||| ||||||||||| ||||||||||||||||||
--gatgtaacctactacct-cacctagtgaagtaa------agctcagttgttgattattagtcattg--gctagtgaatgatgcatttatttttatgctttatgttt------cagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTACGCTGCACTGCG

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G15470.2 (Glycine max), 3'ss of exon 9
gtagttcatctcaccttttgttcctggtta-agcaattactg-aactcattacctacacagtatacattgaagcgattcatttatagcatcaaccatatactgtac--ccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG----------------
                  ||  | || |   |   |||  || |||  | ||||| |||   |||   | ||||   |    ||  | || |  ||| || | |    |  |    | |||||||| || || || |||||||| |||||||| |||||||||||  ||||||| ||||||||||| ||||| ||||||||||||                
-----------------atgagcatgatagcattgattgatgtaacctactacct-cacta-ataggataaagca--ttggctagtgaattatgcatttattttggtgctctatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCGGTGAGTAGGATGAACT

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G15470.1 (Glycine max), 3'ss of exon 9
gtagttcatctcaccttttgttcctggtta-agcaattactg-aactcattacctacacagtatacattgaagcgattcatttatagcatcaaccatatactgta--cccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
                  ||  | || |   |   |||  || |||  | ||||| |||   |||   | ||||   |    ||  | || |  ||| || | |    |  |    | |||||||| || || || |||||||| |||||||| |||||||||||  ||||||| ||||||||||| ||||| ||||||||||||
-----------------atgagcatgatagcattgattgatgtaacctactacct-cacta-ataggataaagca--ttggctagtgaattatgcatttattttggtgctctatgtttcagGTTTTCCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCACCTAGTCTCCGCTGCACTGCG

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G36570.1 (Glycine max), 3'ss of exon 8
---gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtatacattgaagcgatt--catttatagcatcaaccatatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
      |    |||   |  || ||  || ||  |   ||| | |      | || | |   | |   |||  | |     || | || ||||      |  |  | | || ||   | ||||||||||| || || |||||||| |||||||| |||||||||||  ||||||| |||||||| ||||  || || | || ||| 
gtaactgcgtttcttgtcacttctttttgcttttgt--ttaataacagttcttccgagagcttttcttttgggggggcgggcactgat-gcatttg--gtgcaacg-atccatgg--ttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA12G33950.1 (Glycine max), 3'ss of exon 9
gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtatacattgaagcgattcatttatagcatcaacca-tatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
                          || |     || ||    ||| | | |      | |   ||  | | |  | | ||  |   || |   |  |  | | || ||   | ||||||||||| || || |||||||| |||||||| |||||||||||  ||||||| |||||||| ||||  || || | || ||| 
--------------------------gtaactgcgttccttg--tcactccttttggcttttgttttataacaacgcttctactgatgcatctggtgcaacg-atccatgg--ttcagGTTTTTCACAAGCGAATGCCTCCTGAAGCAATTGACCTTGCATCAAGGCTTCTCCAATATTCCCCAAAACTTCGTTACAGTGCA

upper sequence: AT1G06390.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv12s0028g01810.t01 (Vitis vinifera), 3'ss of exon 9
gtagttcatctcaccttttgttcctggttaagcaattactgaactcattacctacacagtatacattgaagcgattcatttatagcatcaaccatatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
            |  |||   |    || ||| |||   |  | |  |||  | | | |||| | |  |   | | |   |||    | ||  | |||   ||   ||    |  |||| ||||| |||||||||||||| |||||  | || ||||| || || ||||||||||||||||| || || ||||||||||| 
---------ggtatgtttgtatatctgtaaaggaatatatatatt--ttattttc-ctgtattcttgtagttggtgcccctat----ttaaaaaaataaaataaaatttgt-tttagGTGTTTCACAAACGGATGCCTCCTGAAGCTCTTGATCTTGCTTCACGACTTCTTCAATATTCACCGAGCCTTCGCTGCACTGCT

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|164004236|gb|ES028603.1|ES028603
EST:     ACTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGCACAAG                         GTTTT-CATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTT
genomic: ACTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGCACAAGgtagttcatc ... tgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTT
EST: gi|124921026|gb|EH994687.1|EH994687
EST:     CTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGGACACAAG                         GTTTTTCATAAACGGATGCCTCCAGAA
genomic: CTACACAGATTTTAGGTTCCCACAAATCAAAGCTCACCCTTGG-CACAAGgtagttcatc ... tgacctccagGTTTTTCATAAACGGATGCCTCCAGAA
EST: gi|125074507|gb|EL138420.1|EL138420
EST:     TCCCACAAATCAAAGCTCACCCTTGGCACAAG                         GTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTT
genomic: TCCCACAAATCAAAGCTCACCCTTGGCACAAGgtagttcatc ... tgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acattgaagcgattcatttatagcatcaaccatatactgtacccttgacctccagGTTTTTCATAAACGGATGCCTCCAGAAGCAATAGACCTTGCATCTCGGCTTCTTCAATATTCACCAAGTCTACGCTGCACTGCG
                                          ccttgac  putative branch site (score: 4)
                                       taccctt  CT-rich tract
           attcatttata  TA-rich tract