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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...catatgcatacaatctcagtcatacctaggtgtgacttgtgaggcaacctcgcgaaattttagcaaatttctggtcttctaaatagcagatcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT

Basic information

species Arabidopsis thaliana
transcript AT4G23470.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G23470.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os10g39100.1 (Oryza sativa), 3'ss of exon 4
-----catatgcatacaatctcagtcatacctaggt-------gtgacttgtgaggcaacctcgcgaaattttagcaaatt---tctggtcttctaa--atagcagatcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT
     ||| ||| |||  |  |   |  | ||   |        |||  |    |       |  | ||| |   |||  |    |   ||  || |  | |    ||   |  ||||| |||||||||||||  ||||| ||||| |||||  | || || ||||||||||||||| | ||||| || ||  | || |||||||||||||||
gtagccatctgcgtactgtagccacccgagctgaatcagttcgatgatctacatgatcttgacatgtaatgtattcaagctgaaccgattcagctgatgaaactgtatttgtttcagGTGTTCTGCTGCTTTGGTAACTCGGTGGCTTCAACCAGGTTCCTGCTGCAAGATGAGTTCAACATTCAGACAACCCAGTGCGACAACTGCATCATT
















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|86038885|gb|DR334640.1|DR334640
EST:     TGGTAGGTGTGGAGA-GCCAAATGTCCTCAACTTTGTCTTTGCCACTGAG                         GTCTTCTGCTGCTTTGGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGC
genomic: TGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTT-GCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTG-CAAACTCTGTGGCCTCAACTCGCTTTCTTCTGC
EST: gi|124839993|gb|EH924432.1|EH924432
EST:     TCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: TCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|116434599|gb|EG477191.1|EG477191
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTTTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|125145835|gb|EL181032.1|EL181032
EST:     TGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTT
genomic: TGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTT
EST: gi|86038879|gb|DR334634.1|DR334634
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|301501098|gb|HO206638.1|HO206638
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|125141539|gb|EL179040.1|EL179040
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAA
EST: gi|86038889|gb|DR334644.1|DR334644
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCC-CTGAG                         GTCTTCTGCTGCTTTGCAAACT
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACT
EST: gi|124988395|gb|EL060784.1|EL060784
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCG
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCG
EST: gi|86038878|gb|DR334633.1|DR334633
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|86038880|gb|DR334635.1|DR334635
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGGCA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTG-CA
EST: gi|86038886|gb|DR334641.1|DR334641
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGC
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGC
EST: gi|86038882|gb|DR334637.1|DR334637
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|164201371|gb|EL968977.1|EL968977
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCC
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCC
EST: gi|86038888|gb|DR334643.1|DR334643
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|301502433|gb|HO207973.1|HO207973
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|86038877|gb|DR334632.1|DR334632
EST:     TGGTAGGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: TGGTAGG-TGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|116434598|gb|EG477190.1|EG477190
EST:     GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
genomic: GTGGTAGGTGTGGAGAAGCCAAATGTCCTCAACTTTGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAA
EST: gi|125228575|gb|EL242660.1|EL242660
EST:     TGTCTTGCCACTGAG                         GTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTC
genomic: TGTCTTGCCACTGAGgtaagaaact ... tcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacctcgcgaaattttagcaaatttctggtcttctaaatagcagatcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT
                               ttctaaa  putative branch site (score: 2)
         aaattttagcaaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
catatgcatacaatctcagtcatacctaggtgtgacttgtgaggcaacctcgcgaaattttagcaaatttctggtcttctaaatagcagatcaatcgcagGTCTTCTGCTGCTTTGCAAACTCTGTGGCCTCAACTCGCTTTCTTCTGCAAGATGAGTTCCAAATTCAAACGACAAAATGTGACAACTGCATCATT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG