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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgttttagatttatctgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg...

Basic information

species Arabidopsis thaliana
transcript AT1G23260.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: LOC_Os03g50440.1 (Oryza sativa), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgttttagatttatctgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg
|||||| || ||||| ||||| || || |||||||||||||||||||||||||| || |||||||  || ||||| || || ||  |||| |||||||||||||||        | | ||   |   | ||   |   ||||   | ||| || |  |    |       |||  |     |||||     |        
TGAGAAGGGCATTGGTGATGGGACAGTGAGCTATGGAATGGATGATGCTGATGACATATATATGCGTTCCTGGACAGGAACTATCATTGGCCCTCCTAATgtatgttgtataacacccattagtagatattaact-gcatttgcttctgtatgctcaaactgaatgatcttttacattcaatttgtcttgcag-------

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G090172_T02 (Zea mays), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatg-tatctctctatcgatctctgagttttgttttagattta-tctgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg
|||||| || ||||| ||||| ||||| |||||||| ||||||||||||||||| || |||||||  || ||||| || || ||  |||||||||| |||||||| |       || | ||   |||| |   |  || ||||  | | |  ||   | |    ||| |   |||    |  || | |   ||         
TGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGATGATGCTGATGACATATATATGCGGTCCTGGACAGGAACTATCATTGGTCCTCCCAATgtatgctgcagaaatacccatag-tgagatacataatacattttctttattattttcaaacctgagaggt--tttactgcgtttattttgcag---------

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GRMZM2G022859_T01 (Zea mays), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatg-tatctctctatcgatctctgagttttgttttagatttatct-gtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg
|||||| || ||||| ||||| ||||| |||||||| ||||| ||||||||||| || | |||||  || ||||| || || ||  |||||||||| || ||||| ||      || | ||  || || |   |  |  |||| | | ||  ||   | |    |||||   ||     || ||||   ||           
TGAGAAGGGCATTGGTGATGGAACTGTGAGCTATGGGATGGACGATGCTGATGACATATTTATGCGGTCCTGGACAGGAACTATCATTGGTCCTCCCAACgtatgctacagaaatacccataact-agatacataatgcatttgttttgttattctcaaacctgagatgt--ttcactgcatttttcgcag-----------

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA05G35000.1 (Glycine max), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgtt-ttagatttatctgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg
|||||| || ||||||||||| ||||||||||||||||||||||||||||||||||| || ||||| || |||||||| || ||| |||| || |||  |||| |     || | ||  |     | || ||||  ||     | || | |   | |  ||| |  |     |||| | |    | |  |||  || |   
TGAGAAGGGAATTGGAGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGATATCTACATGCAGTCCTGGACTGGGACTATTATTGGCCCCCCTGGTgtaagctgtcctgt-tctttggaaaaattgtgttactatgaaaacctctttgcaaaattgtagaacttactatttttatagaaatttatgagttttatcaa

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA07G24950.4 (Glycine max), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttg----ttttagatt-tatctgtgtttgatagagtaaagatgcaa-tttttaacacttttgtgagagaattgttgg
|||||| || ||||| ||||| |||||||||||||||||||||||||||||||| || || ||||||||||||||||| || ||  | ||||| |||| |||| ||  || ||| |   | |       |||        || |   |||  | |||| |    | |  | | || | |||   | ||  ||| | |  |      
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGATGCTGATGACATATACATGCAATCTTGGACTGGGACTATCATCGGTCCCCCTAGTgtaagttgctgtctgttatttttgacacattggaatccccagctaacatccctatttgcttctatgacaaagtaaatattttgaatttcagtgggggctt------

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA08G04710.1 (Glycine max), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgttttagatttatctgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg--
|||||| || ||||||||||| ||||||||||| ||||||||||||||||||||||| || ||||| || |||||||| || ||| |||| || |||  |||| |  | ||| | ||  |     | || ||||  |    || |  | ||||  | | |  |||    ||| ||   |      |   ||| |    ||  
TGAGAAGGGAATTGGAGATGGAACTGTTAGCTACGGAATGGATGATGCTGATGATATCTACATGCAGTCCTGGACTGGGACTATTATTGGCCCCCCTGGTgtaagcttttctgt-tctttggagaaattctgttacaatgataac-atctttgcaaaattgcagaacttattatttttatagaaatttaagagtctacggct

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: GLYMA09G22600.1 (Glycine max), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctga----gttttgttttagatttatc---tgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg
|||||| || ||||| ||||| ||||||||||||||||||||||| ||||| || || || ||||||||||||||||| || ||  |||| || |||  |||| |   ||||||     |||   |      ||| ||||   |||||    | | ||||| | | |  |    | |  |  ||||    | | ||    |      
TGAGAAGGGAATTGGGGATGGAACTGTTAGCTATGGAATGGATGACGCTGACGACATATACATGCAATCTTGGACTGGGACTATCATTGGGCCCCCTGGTgtaagctgctctctgcttttctgaaataataatttatttttcttttattagttatttttgacacattggaatctccagct--aacatccctatcagcttcta-----

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv01s0011g05630.t01 (Vitis vinifera), 5'ss of exon 2
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgttttagatttatctgtgttt-gatagagtaaa--gatgcaatttttaacacttttgtgagaga-attgttgg
 || || || ||||| ||||| ||||| || |||||||||||||||||||||||||| || ||||| || |||||||| || ||  ||||||||||||||||  || | |   | |  |      | |||  |  || | | | ||   |   | | || |      |    || || |  | || ||||   |  ||| |   
GGAAAAGGGAATTGGCGATGGAACTGTCAGTTATGGAATGGATGATGCTGATGATATATACATGCAGTCGTGGACTGGGACTATCATTGGTCCTCCTAATgtgagttttttctttttcaca--caattttcatgatataatgaactccttacaggttgaatctctcaactagatgttaagaatttatgtggttggtattatc--

upper sequence: AT1G23260.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: PP1S490_20V6.1 (Physcomitrella patens), 5'ss of exon 3
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgttttagatttatctgtg--tttgatagagtaaagatgcaattttta-acacttttgtgagagaattgttgg
 |||||||||||||| ||||| || || |||||||| ||||| |||| ||||||  | |  ||||  |||||||| ||||| ||| |||| ||     | ||  || ||  || |  || ||   | ||   |||    |  ||  | |  |   ||    |  ||   |||||  || | | | |   ||   |   |||  
AGAGAAAGGTATTGGCGATGGCACCGTCAGCTATGGCATGGACGATGGTGATGACGTATTCATGCGCTCTTGGACCGGCACTATTATTGGACCAAGCCACgtcagt-tccgtcca--gagctaaaatttacatttcgcgtgaattagcgactcccatcccttttaggcacaattagtagaaaatatcaagactaataagttca

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|116423820|gb|EG466412.1|EG466412
EST:     CACCATTCTTGGTCCTCCTAAT                         ACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
genomic: CACCATTCTTGGTCCTCCTAATgtatgtatct ... cgaatatcagACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
EST: gi|125240891|gb|EL254976.1|EL254976
EST:     CTGGCACCATTCTTGGTCCTCCTAAT                         ACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
genomic: CTGGCACCATTCTTGGTCCTCCTAATgtatgtatct ... cgaatatcagACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
EST: gi|125270405|gb|EL284490.1|EL284490
EST:     ATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAAT                         ACTGCATATGAAGGGAAAATCTTTCAG
genomic: ATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatct ... cgaatatcagACTGCATATGAAGGGAAAATCTTTCAG
EST: gi|86060956|gb|DR356713.1|DR356713
EST:     ATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAAT                         ACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
genomic: ATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatct ... cgaatatcagACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
EST: gi|125173673|gb|EL195061.1|EL195061
EST:     TATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAAT                         ACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
genomic: TATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatct ... cgaatatcagACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
EST: gi|124997604|gb|EL069873.1|EL069873
EST:     CTTGGACTGGCACCATTCTTGGTCCTCCTAAT                         ACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG
genomic: CTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatct ... cgaatatcagACTGCATATGAAGGGAAAATCTTTCAGCTGAAGCTTTTCTGTGGTAAGGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGAGAAAGGTATTGGAGATGGTACTGTTAGCTATGGAATGGATGATGCTGATGATATTTATATGCAATCTTGGACTGGCACCATTCTTGGTCCTCCTAATgtatgtatctctctatcgatctctgagttttgttttagatttatctgtgtttgatagagtaaagatgcaatttttaacacttttgtgagagaattgttgg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgatctct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agtaaaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gagagaat