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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCAGATTTTGGCTGGTGGAAGAGGTCTTGGAACATTCAAGAGTGGTCTTAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtacaggatttcttgtttgtggctttctggagtctgttttttgttgttgttgtacaagttattgatctatttcaaatctttattacttgtag

Basic information

species Arabidopsis thaliana
transcript AT2G20420.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: Vv07s0005g03790.t01 (Vitis vinifera), 5'ss of exon 3
AGCCAGATTTTGGCTGGTGGAAGAGGTCTTGGAACATTCAAGAGTGGTCTTAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtacaggatttcttgtttgtggctttctggagtctgttttttgttgttgttgtacaagttattgatctatttcaaatctttattact-tgtag----
||||| ||| | || |||||  ||||  | ||||||||||| ||||||||||||||||| ||||||||||||||   |||  ||| ||| ||| | ||||||| |    |   | | || | | |   |||           ||||| || |||||     || |  |  | |  ||  ||||| | |||   ||||     
AGCCAAATTCTTGCAGGTGGGCGAGGCTTGGGAACATTCAAAAGTGGTCTTAAGGGTGGAGTTCACATTGTTAAGACTGACCAGGTTGAGGAGCTAGCTGgtaataaggattgtattttatatttcattttaacaccataaatttttttttttgtttccttagct--ttgtttcctttgaatctcttttatcatgtaaaggt

upper sequence: AT2G20420.1 (Arabidopsis thaliana), 5'ss of exon 3
lower sequence: PP1S9_103V6.2 (Physcomitrella patens), 5'ss of exon 3
AGCCAGATTTTGGCTGGTGGAAGAGGTCTTGGAACATTCAAGAGTGGTCTTAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtat--tgtacaggatttcttgtttgtggct--ttctggagtctgttttttgttgttgttgtacaagttattgatctatttcaaatctttattacttgtag-
|| ||  |  |||| |||||  ||||  | || || ||||||| ||| ||||||||||||||||||||||| ||  | ||  |||  || ||||| || ||||     | |      | ||| | |  |||  |||| |||   ||       | | ||| |     || || ||     |       || ||  || ||  
AGTCAAGTGCTGGCAGGTGGTCGAGGGTTAGGTACTTTCAAGAATGGACTTAAGGGTGGTGTTCACATTGTCAAGAGAGACCAGGTGGAGGAGATGGCAGgtacaccctcctttccattttgatagaagctggttctagaggg-gtagaacaatttggttatgttt-ttctttattagactaggcatgttgttgattctatc
















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|116411794|gb|EG454386.1|EG454386
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|116476127|gb|EG518719.1|EG518719
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86046006|gb|DR341761.1|DR341761
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGC
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGC
EST: gi|86045986|gb|DR341741.1|DR341741
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|124823281|gb|EH908147.1|EH908147
EST:     AAGGGTGGTGTTCTACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAG
genomic: AAGGGTGGTGTTC-ACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAG
EST: gi|86045996|gb|DR341751.1|DR341751
EST:     AAGGGTGGTGVTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCCAAGCAAACTGGTCCTCAAGGC
genomic: AAGGGTGGTG-TTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACC-AAGCAAACTGGTCCTCAAGGC
EST: gi|86045998|gb|DR341753.1|DR341753
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86046004|gb|DR341759.1|DR341759
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTC
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTC
EST: gi|86046000|gb|DR341755.1|DR341755
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86046003|gb|DR341758.1|DR341758
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCA
EST: gi|86046005|gb|DR341760.1|DR341760
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86045999|gb|DR341754.1|DR341754
EST:     TAAGGGTGGNGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86045983|gb|DR341738.1|DR341738
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGC
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGC
EST: gi|86045988|gb|DR341743.1|DR341743
EST:     TAAGGGTGGTGTTCACATTGTTAA-CGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTGCACCAAGC
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGT-CACCAAGC
EST: gi|86045982|gb|DR341737.1|DR341737
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAAC
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAAC
EST: gi|86045991|gb|DR341746.1|DR341746
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86045985|gb|DR341740.1|DR341740
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86046002|gb|DR341757.1|DR341757
EST:     TAAGGGTGGTGTTNACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAG-CA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|125245802|gb|EL259887.1|EL259887
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86045989|gb|DR341744.1|DR341744
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86045990|gb|DR341745.1|DR341745
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|116485864|gb|EG528456.1|EG528456
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAGCAAACTGGTCCTCAAGGCA
EST: gi|86045995|gb|DR341750.1|DR341750
EST:     TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTG                         GAAAGATGCTAGGACAAGTACTTGTCACCAAG
genomic: TAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtaca ... ttacttgtagGAAAGATGCTAGGACAAGTACTTGTCACCAAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCAGATTTTGGCTGGTGGAAGAGGTCTTGGAACATTCAAGAGTGGTCTTAAGGGTGGTGTTCACATTGTTAAACGTGATGAGGCTGAAGAGATTGCTGgtattgtacaggatttcttgtttgtggctttctggagtctgttttttgttgttgttgtacaagttattgatctatttcaaatctttattacttgtag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA