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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAGGGAAAATTCAAATAGCCTCAAGAGTGGAGAAGGAATATTTCAAGCCTACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaacttatgaagtcaatgatcttttgtggttatgttttgatgtagcttgcaaatgtctcagctaaaaatttattttgcattgcag

Basic information

species Arabidopsis thaliana
transcript AT1G73020.2
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G73020.2 (Arabidopsis thaliana), 5'ss of exon 13
lower sequence: Vv09s0002g02590.t01 (Vitis vinifera), 5'ss of exon 12
ACAGGGAAAATTCAAATAGCCTCAAGAGTGGAGAAGGAATATTTCAAGCCTACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaa---aacttatgaagtcaatgatcttttgtggttatgttttgatgtagcttgcaaatgtctcagctaaaaatttattttgcattgcag
|||||||| || ||  |  | ||  | || ||||| |||||  | || ||| | ||||||||||| ||||| | ||||||||||||||||||||| ||||||||   |   ||| | ||  |     ||   ||     || | | | | ||   |    |||  |  | ||                       
ACAGGGAAGATCCAGTTCACTTCTCGGGTAGAGAAAGAATACCTGAAACCTTCTTATTCAGCAAGTATTGGAGAAGAACTTGAAGATGGACTTTTTGATGgtaatgcatcaaacctttggggctcccgacaattctcaatt-tctctggctgattcaaataaaattaactgcag---------------------
















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|116436471|gb|EG479063.1|EG479063
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTT
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTT
EST: gi|116435865|gb|EG478457.1|EG478457
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGC
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGC
EST: gi|86080135|gb|DR375892.1|DR375892
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
EST: gi|116436480|gb|EG479072.1|EG479072
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
EST: gi|116436488|gb|EG479080.1|EG479080
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
EST: gi|116436474|gb|EG479066.1|EG479066
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
EST: gi|116436467|gb|EG479059.1|EG479059
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAG
EST: gi|116436479|gb|EG479071.1|EG479071
EST:     TACATATTCAACAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTTTGGAGTGATTATGATGTTTGCTTGTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
EST: gi|116423849|gb|EG466441.1|EG466441
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTG
EST: gi|116423710|gb|EG466302.1|EG466302
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAG
EST: gi|116436486|gb|EG479078.1|EG479078
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
EST: gi|116432871|gb|EG475463.1|EG475463
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAG
EST: gi|116423854|gb|EG466446.1|EG466446
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAG
EST: gi|116435877|gb|EG478469.1|EG478469
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAG
EST: gi|116436469|gb|EG479061.1|EG479061
EST:     TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATG                         ATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG
genomic: TACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaa ... tgcattgcagATTCCCTCGAGCTGGCTTTGCAGTTTGGAATGATTATGATGTTTGCTTGTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACAGGGAAAATTCAAATAGCCTCAAGAGTGGAGAAGGAATATTTCAAGCCTACATATTCAGCAAGCATTGGGGTAGAACTTGAAGATGGACTTTTCGATGgtaagaaaaacttatgaagtcaatgatcttttgtggttatgttttgatgtagcttgcaaatgtctcagctaaaaatttattttgcattgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA