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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaggtttttgaattgcatgtctggtgattgtgcccgttcatgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA

Basic information

species Arabidopsis thaliana
transcript AT1G59610.1
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os06g13820.2 (Oryza sativa), 3'ss of exon 8
aaggtttttgaattgcatgtctggt--gattgtgcccgttcatgtgctgaaggcctttttggatttcggtaaatat-ttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
     |   ||  | ||   ||  |  |||| |   | | | | | || ||   |       ||| |  |||  || |  | |||  || ||||       ||||   |||||||||||||||||||||||||||||| || |||||  |  | || ||| |||| ||  |||| || || |||||| | | |||||| ||||
gttagtaaagagcttcaaacctacttagattttaatcatacct-tcctaaactgcacaagcaattacaataacaatatactgtcttgtataaat-------agGGGTCTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGGAAATTCCCAGAGAGAATTAAACAGCTGCCACTGGACAGGCACTTTGACCTCAGCAATGTTAAAA

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 8
--------aaggtttttgaattgcatgtctggtgattgtgcccgttcatgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
         | | |   | || |  | | |    |   |      | ||||||  || |   |    |||| |    ||   | || |  ||| ||||         |||   |||||||||| |||||||||| ||||| || || || ||  || | |||||| ||||||| ||||| || ||||||||  | |||||||||||||
gttagtgataagctcaagtatggtctttatatataccttaattagt-atgtgccaaatgaaatacctgattac----aaggctgttattcaatcaaaa---------gGGGTCTGGTTGGAAAATTGTTGCAAGCTTTGAGGGGAAGTTTCCAGATAGGATCAAACAGCTTCCTTTGGACAGGCATTTTGATATTAACAATGTCAAAA

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 8
------aaggtttttgaattgcatgtctggtgattgtgcccgttcatgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
      || |   ||  | | ||  | |||| || |||    | | |     ||  |    |   ||| || ||||  |  |||  ||  |   ||| |  |  |||||  ||| |||||| |||||||||||||||||||||| || ||  |  | || ||| |||| ||||||||  ||||||| ||  | ||||| |||||||
gttagtaatgaacttacacttcaaatttggttat-gtggttatacctcc-tagatagttgataatgatgtcagtaacaaagttta-ctgtttttaatgtaat--agGGATCTGGATGGAAAATTGTTGCAAGTTTTGAAGGCAAGTTTCCAGACAGAATTAAACAGCTACCGTTGGACCGACATTTCGATCTCAACAACGTCAAAA

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 8
-----aaggtttttgaattgcatgtctggtgattgtgcccgttca-tgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
      || |  ||  |||    || ||| ||||   ||  |  | ||| |  ||  |||||||    | |    ||  | ||||  | ||     ||   | ||||| | |||||||||||||||||| ||||||||||| ||||| || ||  | |||||  | |||||  | || ||||| |||||| | ||||||||||| |
gaagttagatactttgattttgggtatgg-gatttcaccaatgtactgtacaaaaatccttttttttctgcatctaaattctttcctttat-----ttctttgcagGGTAATGGTTGGAAAGTTGTTGCCAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATTGACAGACACTTTGACATAAACAATGTCAAGA

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 8
-----aaggtttttgaattgcatgtctggtgattgtgcccgttcat-gtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
      || |  ||  |||    || |||  ||    ||  |  |  || |   |  ||| |||    | |    ||  | ||||  | ||     ||   | ||||| | |||||||||||||||||| ||||||||||| ||||| || ||  | |||||  | |||||  | || ||||| |||||| | ||||||||||| |
gaagttagatactttgattttgggtatgggaatc-caccaatgtacagtacaagaatcctattttttctgcatctaaattctttcctttat-----ttccttgcagGGTAATGGTTGGAAAGTTGTTGCTAGTTTTGAAGGGAATTTTCCTAACAGAATCAAGCAACTTCCTATCGACAGACACTTTGACATAAACAATGTCAAGA

upper sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 8
aaggtttttgaattgcatgtc-tggtgattgtgcccgttcatgtgctg----aaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
    || | | ||||  ||   |     |||||| |  | |     |     |    || ||    |  |  | | ||  |  || | |||||  ||   | ||||| || |||||||||||||||||||||||||||||||||||||||||  | |||||  |||| || || |||| |||||||||  | |||||||||||||
----ttctagcattgactgctatcaaccttgtgcaccattagacattacaacagaatctgttctactgcccattattagctg-ctgtcataaattttctttgcagGGTAGCGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAACAGGATCAAGCAGCTACCTTTAGATAAACATTTTGATATAAACAATGTCAAAA

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|125119052|gb|EL167465.1|EL167465
EST:     TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTAGCTGGTGGTGAA                         GGAAGTGGTTGGAAAGTTGTTGCAA
genomic: TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTAGCTGGTGGTGAAgtgagtaatt ... tttggttcagGGAAGTGGTTGGAAAGTTGTTGCAA
EST: gi|125183689|gb|EL198643.1|EL198643
EST:     TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTAGCTGGTGGTGAA                         GGAAGTGGTTGGAAAGTTGTTGCAAGTTTTG
genomic: TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTAGCTGGTGGTGAAgtgagtaatt ... tttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTG
EST: gi|125235693|gb|EL249778.1|EL249778
EST:     TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTGGCTGGTGGTGAA                         GGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTT
genomic: TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTAGCTGGTGGTGAAgtgagtaatt ... tttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTT
EST: gi|125186089|gb|EL201043.1|EL201043
EST:     TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTAGCTGGTGGTGAA                         GGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCA
genomic: TTTGTCGTGAGTTTGAAGACAAATTTCTTCTCCATTTAGCTGGTGGTGAAgtgagtaatt ... tttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA
                                 ctctaat  putative branch site (score: 3)
                      taaatatttttctcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaggtttttgaattgcatgtctggtgattgtgcccgttcatgtgctgaaggcctttttggatttcggtaaatatttttctctaataaaaatttggttcagGGAAGTGGTTGGAAAGTTGTTGCAAGTTTTGAAGGCAATTTCCCCAATCGTATCAAAAAGCTTCCGTTGGATAGACATTTTGACTTGAACAATGTCAAAA

- -gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - - -tttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa