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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcaaacactgaatcgaatataacttgcgttggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT

Basic information

species Arabidopsis thaliana
transcript AT2G30710.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: LOC_Os09g34040.1 (Oryza sativa), 3'ss of exon 9
---------------------------------------------------gtaagcaaacactgaat--cgaatataacttgcgttggtcttgaaaatgttttcttctataaaccacgagaatcaaataca---------agttgtttctgtaaa--caatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
                                                   ||| ||||    || ||  |   |  |          || || | ||||||| ||  | ||||     |    ||| | ||         |||| | ||| ||     |   |||||||| ||  |||||||||| || ||||||||||| ||||| |||||||| || |||||||||||    |||||| |  |||| ||||| || |||||  
gtaagttgaagtaccccttgactgttcataattatttttttcaacttcagtgtatgcaagtgttgcatgcctggtgcaggcaaatgcagttttcacaatgttt-ctggtgtaaatactaatgtccaagtccattgtaattaagttctctctttatttctacctcagTGGTCAGACAAGCTGAAGAAACTTGATTTTCAAGAGATGGTCATGTTCCTTCAGCACCTTCCGACGAGGAACTGGGCTCACCATGAGCTTGAGATGGTGC

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GRMZM2G142806_T01 (Zea mays), 3'ss of exon 10
----------------------------------------gtaagcaaacactgaatcgaatataacttgc--gttggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaaca-atgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
                                                  | |  | | |  | ||  ||   |     |||| ||    || ||| ||   |  |  ||  |||||  |       | |  |   |  ||| ||||||| ||  ||||| ||||||| ||||||||||| ||||| ||||||||||| ||||| || ||    | |||| |  |||| ||||| || |||||  
gtaagtcgctcctgtgaatgatgctaatgttaatttttttcccgtttgttattacaccaacaacaatctgtctgccatgcttgcaa---cttgcttgtaccgatgat-agtttcaaaccctttcctctcccctcctctcatgtagTGGTCGGACAAGCTGCAGAAGCTGGATTTTCAAGAGATGGTGATGTTCCTGCAGCACCTCCCCACGAGGACCTGGGCGCACCACGAGCTGGAGATGGTCC

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA13G42180.1 (Glycine max), 3'ss of exon 9
gtaagcaaacactgaatcgaatataacttgcgt-tggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatg-cagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
    ||||    |    |    |  ||||  |       |||  |||| ||   | |  |  | | ||  |  |    | | |  ||    |      |  |||||||||||  | ||  ||||||| ||||| |||||  ||||||||||||| ||||||||||| ||  | |||||| | ||||| |||||||| |||||  
---tgcaatttttttgccagtaaacacttctgcaccactttgtgaatgcttctatttccac-ctaggatgaatattctctaatctttataattgtttttatcagTGGTCTGACAATCTCCAGAAGCTTGATTTCCAAGAGTTGGTAATGTTCCTTCAACACCTTCCAACTAAGAACTGGACTGACCAGGAGCTCGAGATGGTAC

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA15G03200.1 (Glycine max), 3'ss of exon 9
gtaagcaaacactgaatcgaatata-acttgcgt-tggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatg-cagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
    ||||    |    | | || | ||||  |       |||  |||| ||   | |     | | ||  |  |    | | |  || |  |      |  |||||||||||  ||||  ||||||| ||||| ||||| |||||||||||||| || |||||||| ||  | |||||| |  | || |||||||| |||||  
---tgcaacttttttgcc-agtacacacttctgcaccactttgtcaatgcttctatttcccc-ctaggatgaatattctctaatctttacaattgtttttatcagTGGTCTGACAAGCTCCAGAAGCTTGATTTCCAAGAGATGGTAATGTTCCTTCAGCACCTTCCAACTAAGAACTGGACTCAACAGGAGCTCGAGATGGTAC

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA11G13330.1 (Glycine max), 3'ss of exon 9
-----gtaagcaaacactgaatcgaatataac--ttgcgttggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
      |    |    || |    | |   ||  |   |||| | |||  |||| ||  ||   ||        |||   |||     || |   | |   |  |  ||||||| ||  ||||  |||| ||  |||| |||||| ||||||||||||| ||||||||||| ||| | |||||| |  |||  ||||| || |||||  
aatttatgtatagttgcttaggttatttacacggtcttgttgcttttggcaatgcttaatttagtag-------gaactgaattttctttttactttttccc--tttagTGGTCAGACAAGCTCCAGAAACTTCATTTCCAAGAATTGGTAATGTTCCTTCAACACCTTCCAACAGAGAACTGGACTCACCGGGAGCTTGAGATGGTGC

upper sequence: AT2G30710.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv05s0094g00070.t01 (Vitis vinifera), 3'ss of exon 9
-gtaagcaaacactgaatcgaatataacttgcgttggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
 ||  |       |       | ||  |||  |      | |||  |   ||   | || || |||   || ||  |  |   ||||| |        | |||||||| |||  |||  ||||||| ||||| |||||  ||||||||||||| ||||||||||| || ||||||||| |  ||||||||||||| |||||  
tgtttgtgttttttttccttgagatttctt-tgcacaattagaagctagattaagc-atgaaacactt-aaccatgtgtacactgttttttgtttgttttcagTGGTCGGATACGCTTCAGAAGCTTGATTTCCAAGAGCTGGTAATGTTCCTTCAACACCTTCCAACTCATAACTGGACTCACCAAGAGCTCGAGATGGTGC

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|125133947|gb|EL175142.1|EL175142
EST:     ATGCGTTGCCAGACTTCCTGGTGTATATATATGCTAGCTTTCTCTTGACG                         TGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAA
genomic: ATGCGTTGCCAGACTTCCTGGTGTATATATATGCTAGCTTTCTCTTGACGgtaagcaaac ... aacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAA
EST: gi|86086042|gb|DR381801.1|DR381801
EST:     ATGCGTTGCCAGACTTCCTGGTG--TATATATGCTAGCTTTCTCTTGACG                         TGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTG
genomic: ATGCGTTGCCAGACTTCCTGGTGTATATATATGCTAGCTTTCTCTTGACGgtaagcaaac ... aacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT
     ttctataaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcaaacactgaatcgaatataacttgcgttggtcttgaaaatgttttcttctataaaccacgagaatcaaatacaagttgtttctgtaaacaatgcagTGGTCTGATGAGCTGAAGAAGCTAGATTTTCAAGAAATGGTAATGTTCCTGCAACACCTTCCGACACATAACTGGTCAGACCAAGAGCTCGAAATGGTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT