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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaatttattaatttttccatatatatgaaa...

Basic information

species Arabidopsis thaliana
transcript AT2G46770.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os08g02300.1 (Oryza sativa), 5'ss of exon 1
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaatttat--taatttttccatatatatgaaa--------------------------------------------------
 |  | || || ||||| ||||| ||      |    ||||||| || || ||||| |||||||| || ||||||||||||||||| |||||||| ||||||      | |       |||  | || |  |||  ||    || ||  | ||||| | | | |  | || |||  ||  |   |||  ||   |   ||                                                    
CTCAACTACTACCTCCGCAAGAAGGTCGCCTCCGAGCAGATCGACCTCGACGTCATCCGCGACGTCGACCTCAACAAGCTCGAGCCATGGGACATCCAAGgtag----ctaagctagtattcctcatcatataacctttctcctctccaattctca-atttctagctaccaaatcgatgatggatttatcaatcaatcgagctaagctagctaagtaatggtgtgtgtgcaaaatatatattgtggttgcag

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: LOC_Os06g04090.1 (Oryza sativa), 5'ss of exon 1
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaatttattaatttttccatatatatgaaa
 ||   || || ||   |||||| ||             ||||| || || ||||| |||||||| || ||||||||||||||||| |||||||| ||||||   |    || ||| |       ||  || ||||   ||  |||   ||     |    |||| |  |   | | |    |  | |||| ||||| | 
CTGACATACTACCTGAAGAAGAAGGTGGCCTCGGAGCGCATCGACCTCGACGTCATCCGCGACGTCGACCTCAACAAGCTCGAGCCATGGGACATCCAAGgtacgta---attaagcacacacacatcgatcaattcgatcgatttttgacatgttttgatcaatgtggcatgtgtgta---tcatacatacatatgcag

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G069047_T01 (Zea mays), 5'ss of exon 1
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgt-----ttatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaattta-ttaatttttccatatatatgaaa---------------------------------------------------------------------------------
 |  | || || ||||| ||||| ||      |    ||||||| || |||||||| |||||||| || ||||||||||||||||| |||||||| ||||||      || || |    | | |  ||  ||     |  |          ||    ||| | |||  |   || ||    |  |  |      ||    |||  |                                                                                 
CTCAACTACTACCTCCGCAAGAAGGTGGCCTCCCAGCAGATCGACCTCGATGTCATCCGCGACGTCGACCTCAACAAGCTCGAGCCATGGGACATCCAAGgtacggtatacttaccaccatataccttccatctccgaggtccgagcaaagcatcagctcgtgatcataggatcggatcggagctggtgacctgatggtcatgtcacacgagcatgaacgtgagctgatcatcgtacgtccatggcgctgatcatcggggttagttatcgattctgcgtgcatgcag

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G092465_T03 (Zea mays), 5'ss of exon 1
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaagaa---attttttatgaattaat-tttctctctttcacactctcataatccaattttc-cgaatttattaatttttccatatatatgaaa
 |  | || || ||||| ||||| ||      |   |||||||| || || ||||| |||||||| || ||||||||||||||||| |||||||| ||||||   |    |   |       |    |  ||     |    ||  |||   ||   |||   || |     | ||     | ||      |      |      
CTCAACTACTACCTCCGCAAGAAGGTGGCCTCCCAGGAGATCGACCTCGACGTCATCCGCGACGTCGACCTCAACAAGCTCGAGCCATGGGACATCCAAGgtacgtacgtacgcacggccggtccggtccgatccggtaccactgccttcttcaacttcaagttcaagcacgcgcgcgcgcagtagcagagcagctcgtg-----

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GRMZM2G091490_T01 (Zea mays), 5'ss of exon 1
TTGCAGTATTATCTCCGGAAGAAAGTTA-ATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaa-------gaaattttttatgaatta-attttctctctttcacactctcataatccaattttccgaatttattaatttttccatatatatgaaa----------------
 ||   || || ||   |||||| ||    | | | ||  ||||| || || ||||| |||||||| || ||||||||||| ||||| |||||||| |||||| |   |||||  |       | |  | | || ||   | ||      || |   |  ||||||          | | |||  || ||  || | ||    | ||                  
CTGACCTACTACCTGAAGAAGAAGGTGGCGTCGGAGCGC-ATCGACCTGGACGTCATCCGCGACGTGGACCTCAACAAGCTGGAGCCATGGGACATCCAAGgtatgcatccatgcatatagtaggatctgtgtacgagacacatgcatgatcatcgtctatctcattgcttgcgcatgc-aatgcatgaaacttac-atggcgacgaccggactgacccctgcag

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G44910.1 (Glycine max), 5'ss of exon 1
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaatttattaatttttccatatatatgaaa
|||||||| ||| |  |||||||  |    | |    ||||||| || || || |||||||| ||||||||||||| |||||| || |||||||| ||||||            |  | ||||||   || ||  |           | |   | |      | |      |||| |||||||| | ||           
TTGCAGTACTATTTGAGGAAGAAGATGTCCAACGAGAAGATCGACCTCGACGTGATTCGCGATGTTGATCTCAACAGGCTCGAACCATGGGACATACAAGgt-----------gatgatttttttgctaagtagcta----------agataattaatgagtagtgcatgtaattgattaatttgtgcag----------

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA19G44890.1 (Glycine max), 5'ss of exon 1
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaatttattaatttttccatatatatgaaa
|||||||| ||| |  ||||||| ||    | |    ||||||| || || || |||||||| |||||||||||||  ||||| || |||||||| ||||||           | ||  ||||||    | ||         ||   | | | | || |   | |      |||| |||||||| | ||           
TTGCAGTACTATTTGAGGAAGAAGGTGTCCAACGAGAAGATCGACCTCGACGTGATTCGCGATGTTGATCTCAACAGACTCGAACCATGGGACATACAAGgt----------gatgattttttttgctcagtag--------ctaagataat-tgatgagt-agtgcatgtaattaattaatttgtgcag----------

upper sequence: AT2G46770.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: PP1S161_73V6.1 (Physcomitrella patens), 5'ss of exon 2
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtt--tatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaatttattaatttttccatatatatgaaa------------------------------------------------------------------------------------------------
 ||   ||||| || |  |||||||| |    |    ||||||| |||||| ||||||||||| | |||||  ||||||| ||||| |||||  ||||||||   ||    |  |  | | |||||| |   ||  |||| | | ||| |  |      |||  | |  |   ||  ||| |||   | || |  |  |||                                                                                                 
GTGGGCTATTACCTTCCTAAGAAAGTCACAGCCCGGAAGATCGACCTTGATCTCATTCGCGACCTAGATCTTTACAAGCTTGAGCCGTGGGATCTTCAAGgtcagtacaaactcattgcagtttttttt---ttgtttttgtttttttaaagc------aatttactcgttgaaagatatcaatagattcagaagtcagaacagagtataggatttgatcaaaaaccccacaacctgacattgaattcgactctgttcatcctcatctaaacatccgatggtctctttcatggaacag

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|86053372|gb|DR349129.1|DR349129
EST:     TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAG                         AGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCC
genomic: TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttcc ... cgttatgcagAGATGTGTAAAATAGGAACAACGCCACAAAACGACTGGTATTTCTTTAGCC
EST: gi|19875621|gb|AU236452.1|AU236452
EST:     TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAG                         AGATGTGTAAAATAGGAACAACGCCACA
genomic: TGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttcc ... cgttatgcagAGATGTGTAAAATAGGAACAACGCCACA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTGCAGTATTATCTCCGGAAGAAAGTTAATAGCATCGAGATCGATCTTGATGTCATTCGCGACGTTGATCTCAACAAGCTCGAGCCTTGGGACATTCAAGgtttatttccataaagaaattttttatgaattaattttctctctttcacactctcataatccaattttccgaatttattaatttttccatatatatgaaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cactctca