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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtaaatcgccgaatgattgctcatgttgctacttatatattggtcaaaacataattctgacgtgggtataatgcattgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTGGACAGAGGTTATACTTCACCATACTTTATCACTAATCAAAAAACCCAAA

Basic information

species Arabidopsis thaliana
transcript AT3G23990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv05s0051g00340.t01 (Vitis vinifera), 3'ss of exon 6
---------------gtaagtaaatcgccgaatgattgctcatgttgctacttatatattggtcaaaacat--aattctgacgtgggtataatgcattgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTGGACAGAGGTTATACTTCACCATACTTTATCACTAATCAAAAAACCCAAA
                | | |  |      | |  |   |  || ||    || || ||||  | | |  |  || |||  |   ||   | ||  ||||||||||| |||||||||| ||| || ||||||||||| |||||||||||  |||| |||||||| |  || || || ||||| || || || ||||||||||
ttttcttttattttttttattttaatatttattcttatattttgctgaattttttaaattgcactatatgtctaactctttccatggggaattg--ttgcagGATGGGAAGACATTGTATAATGAATTGGAAGTTGTTGAGGGGATGAAGCTGGATAGAGGTTACATATCCCCTTATTTTATAACAAACCAGAAAACCCAAA

upper sequence: AT3G23990.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: PP1S149_289V6.1 (Physcomitrella patens), 3'ss of exon 6
---gtaagtaaatcgccgaatgattgctcatgttgctacttatatattggtcaaa----acataat--tctgacgtgggtataatgc------attgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTGGACAGAGGTTATACTTCACCATACTTTATCACTAATCAAAAAACCCAAA
     |||     |     |  |||               || || | | | |||    |  ||||  ||    |  | | | |||       ||  |||||||||||||| || ||||| |||||||| ||||| ||||| |||||  | ||||| || |||| ||| || || || |||||||||  ||| ||||| |
cccacaaggtctccattctagcattatgtgccagagggtatagatttcgattaaatgccatctaatggtccagtgatgttctcatgtggtattatcacagGATGGAAAGACTTTATTTAATGAGTTGGAGGTTGTGGAGGGCATGAAGCTTGACAGGGGATATATTTCCCCCTATTTCATCACTAATGCAAAGACCCAGA
















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|86027480|gb|DR323233.1|DR323233
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAAGGTGTTATCACAATCCAA                         GATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAA-TTG
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAAGGTGTTATCACAATCCAAgtaagtaaat ... tgcattgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTG
EST: gi|124928092|gb|EL005766.1|EL005766
EST:     GCTATGGAGAAGGTTGGCAAAGAAGGTGTTATCACAATCCAA                         GATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTG
genomic: GCTATGGAGAAGGTTGGCAAAGAAGGTGTTATCACAATCCAAgtaagtaaat ... tgcattgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTG
EST: gi|86027481|gb|DR323234.1|DR323234
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAAGGTGTTATCACAATCCAA                         GATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAAGGTGTTATCACAATCCAAgtaagtaaat ... tgcattgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctacttatatattggtcaaaacataattctgacgtgggtataatgcattgcagGATGGAAAGACATTGTTTAACGAGTTGGAAGTTGTAGAGGGGATGAAATTGGACAGAGGTTATACTTCACCATACTTTATCACTAATCAAAAAACCCAAA
                            ttctgac  putative branch site (score: 2)
                   aaaacataatt  TA-rich tract