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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag

Basic information

species Arabidopsis thaliana
transcript AT2G37270.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os01g01060.1 (Oryza sativa), 5'ss of exon 3
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag
| || ||||| ||  | ||   ||||||||| ||||||||||| || |||||||||||||||||||| ||||||||||| || ||||| || ||||||||||||             |  | |  | ||  ||||||   | |   || ||  |  |   |   |||||  |   || ||              
TCACCACTGGCGCCAGGGAGAGTGCCTTTAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGATGAGCTCATCAATGCCGCCAAGGGCTCATCCAACAGgtaa-------------atcttgcttctcatttgatgaaatgaggctactgacacatccatgctctaattctgatatgttacag----------

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os11g29190.4 (Oryza sativa), 5'ss of exon 3
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag
                 ||    ||||| || ||||||||||| || ||||||||||||||||| || || || ||||| || ||||| || |||||||||||  |||||  | ||   || ||   |||     |   |||   | ||     |||| || |   |    |   ||||  |  ||| |     
----------------GGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAGgtac-aacacattgtc---atggtacatcttgctttttgttcggatgataccaggtta-ttgacacatctgtg--atctaattgtgtttcag--

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os11g29190.2 (Oryza sativa), 5'ss of exon 3
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag
| || ||||||||  | ||    ||||| || ||||||||||| || ||||||||||||||||| || || || ||||| || ||||| || |||||||||||  |||||  | ||   || ||   |||     |   |||   | ||     |||| || |   |    |   ||||  |  ||| |     
TCACCACTGGTGCCAGGGAGAGCGCCTTCAGGAACATCAAGACCATTGCTGAGTGCCTTGCTGACGAGCTTATTAATGCCGCCAAGGGCTCATCCAACAGgtac-aacacattgtc---atggtacatcttgctttttgttcggatgataccaggtta-ttgacacatctgtg--atctaattgtgtttcag--

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G078985_T01 (Zea mays), 5'ss of exon 3
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttat-tgtta-gttagttaagctaataatagcatcttctcttgtcttgcag
| || ||||||||  | ||    || || || |||||||| || || |||||||||||||| |||||  | ||||| ||||| ||||| ||||||||||||||   | |  || |||     | || | | | | ||  ||     ||| ||  | || | ||  ||| ||  |     |   |||||||   |||
TCACCACTGGTGCCAGGGAGAGCGCTTTCAGGAACATCAAAACCATTGCTGAGTGCCTTGCAGATGAGTTGATCAACGCTGCCAAGGGCTCTTCCAACAGgtatatatatcctgtct-----ggctatatttggttgtttttttcctatctgcgatgtgaattgtgctcat--tcatggcaattcttgtc--acag

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G156673_T03 (Zea mays), 5'ss of exon 2
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag
| || ||||||||  | ||   ||| ||  | |||||||| || || || ||||||||||| ||||| || ||||| ||||| ||||| || |||||||||||   |   |   | |        ||||| |   ||  | | |   || || |  | |||   || ||  | |   |   ||||||  | |||
TCACCACTGGTGCCAGGGAGAGTGCTTTCCGGAACATCAAAACCATTGCCGAGTGCCTTGCAGATGAGCTGATCAACGCTGCCAAGGGCTCATCCAACAGgtacatatgttgcctgtttgcttcttgtctatctgtgattccgcacgat-gtgaaattgtt---ctcat--tcgtgccaattcttgt--tacag

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA12G32850.1 (Glycine max), 5'ss of exon 4
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactcta--tctacatagtc-tgtctcttgatg-gcttcactttatt-gttagttagttaagctaataatagcatcttctcttgtcttgcag--------------------
| |||||||||||||| |||||||| || ||||| || |||||||| ||||| ||| | ||||||||||| || ||||| ||||| || || |||||||||||          |  ||||  | |     | |  |||||   || | ||| ||  |   ||   |    |  || | |  | |    || | |  |                      
TAACAACTGGTGCACGCGAAGCTGCTTTCAGAAATATTAAGACAATTGCTGAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCGTCCAACAGgtatacttctaggaattctatgtggaggcattttctgatgtattttattttcttcatctctttcatttttttttattggtgtttgggtttttttaccgaaaaataatactccatttcag

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA13G37610.1 (Glycine max), 5'ss of exon 4
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgta-------agaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag-----------------
| |||||||| ||||| |||||||| || ||||| || |||||||| || || ||| | ||||||||||| || ||||| ||||| || || |||||||||||       | ||   | ||| |  |   |     |  |||||  ||   | |  | |  ||   | |   |  |||| | |  ||   ||  ||   |                  
TAACAACTGGAGCACGGGAAGCTGCTTTCAGAAATATTAAGACAATTGCAGAATGCTTGGCTGATGAACTTATTAATGCAGCAAAAGGGTCATCCAACAGgtatacttctaaaattttatatgtggaggatacagtttctgatgtattttatcttctat--gtctttcatttttctaattggagtttgggttcactgaaaaataatactccatttcag

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: PP1S400_33V6.1 (Physcomitrella patens), 5'ss of exon 3
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactct-------atctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataa-tagcatcttctcttgtcttgcag
| || ||||| ||||| ||  |||| ||||||||||||||||| || ||||||||| | ||||||||  | || || || || ||||| || || |||||||| ||| | |          ||| |    | |   | ||  | |   ||    |||||||           |  | | | |    |  |  | | || |||
TCACCACTGGCGCACGAGAGTCTGCTTTTAGAAACATCAAGACCATTGCTGAGTGCTTGGCTGATGAGTTGATTAACGCAGCCAAGGGTTCCTCAAACAGgtatgaatagttacgggaaagtcttcgacatttacttgttctttggagcagaa-attgttatcctaccctttttctgacttgtgggtaattcttttttacag

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ17708 (Selaginella moellendorffii), 5'ss of exon 4
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag
| || ||||| || || ||   ||| ||  ||||||||||||| ||||| |||||||||||||| || ||||| ||||| || ||||||||||||||||||||    |       | | | | |||  |||| |         || ||  |||  ||  ||  | |  |   ||                    
TCACTACTGGAGCTCGCGAGAGTGCTTTCCGAAACATCAAGACCATCGCCGAGTGCCTTGCTGACGAGCTCATGAATGCCGCCAAGGGATCTTCCAACAGgta----cctcgcggccagaaattcttcctctcgcc--tcaagctctaaagttccttgtttttgatgttt-cag--------------------

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ16239 (Selaginella moellendorffii), 5'ss of exon 4
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag
| || ||||| || || ||   ||| ||  ||||||||||||| ||||| |||||||| ||||| || ||||| ||||| || ||||||||||||||||||||    |  |    | | | | ||| ||||| |         || ||  |||  ||  ||  | |  | || |  ||                
TCACTACTGGAGCTCGCGAGAGTGCTTTCCGAAACATCAAGACCATCGCCGAGTGCCTCGCTGACGAGCTCATGAATGCCGCCAAGGGATCTTCCAACAGgta----ccttgcggccagaaattctttctctcgcc--tcaagctctaaagttccttgtttttgtttttgat-gtttcag--------------

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ37091 (Selaginella moellendorffii), 5'ss of exon 4
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagt-ctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag
| || ||||| || || ||   ||| ||  | ||||||||||| ||||| |||||||||||||| || || || ||||||||||||||||| |||||||||||        ||  |||||| || ||  ||| || |   |  |    | |   || |  ||  |    |  | |||||                
TCACCACTGGAGCTCGCGAGAGTGCTTTCCGTAACATCAAGACCATCGCCGAGTGCCTTGCTGACGAGCTGATGAATGCTGCAAAGGGATCGTCCAACAGgta--------cttcctacattgttctagctcatgct--ttgaaagaaactaagagctccttctgtgcttgtttgcatcag--------------

upper sequence: AT2G37270.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: EFJ18003 (Selaginella moellendorffii), 5'ss of exon 4
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag---
| || ||||| || || ||   ||| ||  | ||||||||||| ||||| |||||||||||||| || || || ||||||||||||||||| |||||||||||        ||  |||||| ||               |  |  | ||  || |  ||  || |||| |    | |||   ||||| |||||    
TCACCACTGGAGCTCGCGAGAGTGCTTTCCGTAACATCAAGACCATCGCCGAGTGCCTTGCTGACGAGCTGATGAATGCTGCAAAGGGATCGTCCAACAGgta--------cttcctacattgt---------------tctagctcatgctttgaaag--aaactaagagccccttctgtgcttgt-ttgcatcag

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|86075624|gb|DR371381.1|DR371381
EST:     GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
EST: gi|301501481|gb|HO207021.1|HO207021
EST:     GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
EST: gi|164084436|gb|ES116286.1|ES116286
EST:     ATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: ATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
EST: gi|86081297|gb|DR377054.1|DR377054
EST:     GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAG                         CTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG
genomic: GAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacac ... tgtcttgcagCTATGCCATCAAGAAGAAAGATGAGATTGAGAGAGTTGCTAAGGCCAATCG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTACAACTGGTGCACGTGAAGCTGCCTTTAGAAACATCAAGACAATCGCTGAGTGCCTTGCTGATGAACTCATCAATGCTGCAAAGGGATCTTCCAACAGgtaagaacactctatctacatagtctgtctcttgatggcttcactttattgttagttagttaagctaataatagcatcttctcttgtcttgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG