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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttctatgttctttaagtatgtaaagtttgagttgtgatcgttgctttaaagggtcattgttagtagcatacttgtgtgattcattttgttcata...

Basic information

species Arabidopsis thaliana
transcript AT3G23490.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G23490.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os10g33270.1 (Oryza sativa), 5'ss of exon 2
GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaag-tttctatgt-tctttaagtatgtaaagtttgagttgtgatcgttgctttaaagggtcattgttagtagcatacttgtgtgattcattttgttcata
 ||||||||||| || ||||||||||| ||||| || ||||| ||||||||||| || ||||| ||||| ||||||| | |||   | |  || | | | |    |||   ||     |  |  ||       ||  ||||  | | |        ||    |  ||    || 
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGTGATGGAATgtaagatatctgcctatgcttcattctatttgattttcatttaccccagtatttcttgacttc-ctgttcctggtaactgcacatggacgaagttaaggat-

upper sequence: AT3G23490.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G134747_T01 (Zea mays), 5'ss of exon 2
GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaag---tttctatgttctttaagtatgtaaagtttgagttgtgatcgttgctttaaagggtcattgttagtagcatacttgtgtgattcattttgttcata--
 ||||||||||| || ||||||||||| ||||| || ||||| || |||||||| || ||||| ||||| |||||||   |  |  || |   |   |   |||| |     |  || |  |  ||   | |    ||| |  ||   ||| ||  || | ||  || |||   |  
ATTGAATGAAGCTGTTATGCATTTTGGAGAGAGCATCAAGGAAATCATCAATGAGGAGTTTGGTGATGGAATgtaagagataccagtgcttcatttatgcataaattcctgttcctggtaat--ctggcatgaactattat--gtgatatagtta-gtaaatccattagttatgatt

upper sequence: AT3G23490.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA10G00790.1 (Glycine max), 5'ss of exon 2
GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttctatgttctttaagtatgtaaagtttgagttgtgatcgttgctttaaagggtcattgttagtagcatacttgtgt--gattcattttgttcata
|||||||||||| || ||||||||||| ||||| || || || || |||||||| || ||||| ||||| ||||||||||| ||    |     ||| |      ||| |  | |   |    ||    |||  || |   ||    ||||| ||    |  ||  ||||    
GTTGAATGAAGCTGTTATGCATTTTGGGGAGAGCATCAAAGAAATAATCAATGAGGAGTTTGGTGATGGGATgtaagtttcaattacataatgatatatttctcatgaatgctcaagatgaagttgtttggtgtttttctatatatgacttgagttgagtgtatcatgtttt--

upper sequence: AT3G23490.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv05s0049g01520.t01 (Vitis vinifera), 5'ss of exon 2
GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttctatgttctttaagtatgtaaagtttgagttgtgatcgt-tgctttaaagggtcattgttagtagcatacttgtgtgattcattttgttcata
 ||||||||||| |||||||||||||||||||| || ||||| ||||||||||| || ||||| |||||||||||||| | | || |||   | | | |   |||||  |      | | | ||||  ||  |  |||  |   |  |           |        |   |
ATTGAATGAAGCCGTGATGCATTTTGGTGAGAGCATCAAGGAAATTATCAATGAGGAGTTTGGCGATGGCATgtaagtctttttggtctcccaatttctct-gtttgcttgccacacatgtacttttgagcctgtttgacaacggtttctgaaaacaggtttcccaaatttca

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|125022477|gb|EL094746.1|EL094746
EST:     TTATCAATGAAGATTTTGGAGATGGCAT                         CATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAA
genomic: TTATCAATGAAGATTTTGGAGATGGCATgtaagtttct ... gtttgtttagCATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAA
EST: gi|86077490|gb|DR373247.1|DR373247
EST:     TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT                         CATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGGAGTGGA
genomic: TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttct ... gtttgtttagCATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGGAGTGGA
EST: gi|116453344|gb|EG495936.1|EG495936
EST:     TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT                         CATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGGAGTGGA
genomic: TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttct ... gtttgtttagCATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGGAGTGGA
EST: gi|124824752|gb|EH909618.1|EH909618
EST:     TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT                         CATGTCGGCGATAGATTTCTATTGCTCTGTCGAACAAAAT
genomic: TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttct ... gtttgtttagCATGTCGGCGATAGATTTCTATTGCTCTGTCGA-CAAAAT
EST: gi|124726811|gb|EH818213.1|EH818213
EST:     TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT                         CATGTCGGCGATTGATTTCTATTGCTCTGTCGACAAAATCAAAGG
genomic: TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttct ... gtttgtttagCATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGG
EST: gi|125291247|gb|EL305332.1|EL305332
EST:     TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT                         CATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGG
genomic: TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttct ... gtttgtttagCATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGG
EST: gi|116453343|gb|EG495935.1|EG495935
EST:     TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCAT                         CATGTCGGCGATAGATTTTTATTGCTCTGTCGACAAAATCAAAGGAGTGGA
genomic: TTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttct ... gtttgtttagCATGTCGGCGATAGATTTCTATTGCTCTGTCGACAAAATCAAAGGAGTGGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTTGAATGAAGCAGTGATGCATTTTGGTGAGAGTATAAAGGAGATTATCAATGAAGATTTTGGAGATGGCATgtaagtttctatgttctttaagtatgtaaagtttgagttgtgatcgttgctttaaagggtcattgttagtagcatacttgtgtgattcattttgttcata

- - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG