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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

Basic information

species Arabidopsis thaliana
transcript AT5G16540.3
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os11g28270.1 (Oryza sativa), 3'ss of exon 6
-----------------gtaagctaataaaagacttcagattctttcc-tttatagtctcattatgtggtttggtaaattcttgttgctggtttgaa---acagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
                   || |  |||||| |    | || | | |  | || |   |    | ||| ||   |||     |||| ||  ||        |||||||| ||  | |||   ||||||||||| ||||| ||||||||||||||||| |  || ||||||||||| || ||| ||    | |  ||      | 
gtttatcatgcaatgttcaaaaccgataaaacat---aaatacatacaatatagaagatggacaagtg-ttgcctaatcctctgtttctttttcctgcttgcagGGAGAGCCCATATGCACATTCTATTCTCGCTATGGCATCTGCAAGTTTGGTCCGAATTGCAAATTTGATCATCCAATGGGAACTGTGATGTATGGTCTCG

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os12g21700.1 (Oryza sativa), 3'ss of exon 6
-----------------gtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
                  |||      |  |  ||  |  ||  | | |||    | ||      || |    |||  |||   |  |   |   |||||||||||||  | |||   ||||||||||| || |||||||||||||||||||| |  || |||||||| || || ||| ||  | | |  ||    |   
agtagttccaataaattataatacttgagtaatctgtaatttggtactttttgcctatcgggggatgctaccctaacatctatctctttcctgctaacagGGAGAACCTGTCTGCACATTCTATTCTCGTTACGGGATCTGCAAGTTTGGTCCTAATTGCAAATTTGACCATCCTATGGGAACCCTTATGTATGGAAGTG

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: LOC_Os01g68860.3 (Oryza sativa), 3'ss of exon 5
-----gtaagctaataaaagacttcagattct-----ttcctttatagt-ctcattatgtggtttggtaaattct--tgttgctggtttgaaa----cagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-
      ||   || ||  |   || | | |         | || || || |  || |       || |  | | |      |||| || || |    |||||||||  |||||||  |||||||||||| ||||| ||||||||||| ||  | |  || |||||||| || || | |   | || | |  |    |    
actgtatatattagtatgaagattaacacttgaaaaaacctttgattgttcctataacacctaatgattgactatgacacggctgtttcgagattttcagGGAGAAGAACTGTGCAAGTTCTATTCTCGCTATGGCATCTGCAAGTTCGGCGCGAATTGCAAATTTGACCATCCAACGATGG-CTCCTCCAATGGGAGTGT

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GRMZM2G107491_T03 (Zea mays), 3'ss of exon 6
------------gtaagctaataaaagacttcagattctttcctttata-gtctcattatgtggtttggta----aattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-
             |     |  || || |   || |  |     |  ||   ||||||   |||| ||  |     ||| |  |  |   |       |||| |||  ||| |||   ||||||||||| ||||| ||||||||||| ||  | | ||||||||||||||| || |     | || | |  |    |    
tacaaataaagcctgtctcacgaataggcactagctagtccttctggtacacctcattgaatggtctgccatcttgattatcctgtccaatggtttttagGGTGAAGAACTTTGCAAATTCTATTCTCGTTATGGCATCTGCAAGTTCGGCGCCAACTGTAAATTTGATCATCCTACAATGG-CTGCTCCAATGGGAGTTT

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA18G47660.1 (Glycine max), 3'ss of exon 6
-gtaagctaataaaagacttcagattctttcctttatagtctcat-----tatgtggtttggtaaattcttgttg----------ctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA-
  | ||   |||    | |    ||| | | |    |  | | ||     |||    || |||| || ||  | |          |   |||   ||||||||| || ||||| ||||||||||| || ||||| || ||||| |||||||||||||| || ||||||||||| ||| |||||||||| || ||||    
gatgagaatatatgcaattcagtattgtcttcacactgatttgatatttttattgatttcggtacatgctaatagaggttgtgtcccattttcctacaggGAGAGCCCCTGTGTGTGTTCTATTCACGTTATGGCATATGCAAATTTGGTCCAAGCTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATGTC

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G38650.2 (Glycine max), 3'ss of exon 6
--------------gtaagctaataaaagacttcag-attctttcctttatagtctcattatgtggt--ttggtaaattcttgt-tgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
               || || |||     | | |||  |||| | |    |  | |   ||  || |  | |   |    |||| | |   |||   ||||||||| || ||||| ||||||||||| || || || || ||||| ||||||||||| || || ||||||||||| ||| |||||||||| || ||||   
agggagatgagaatatatgc-aattgtttattacagtgttctcttcacattgattttggtacatgctaatagaggagaggttgtgtcccattttcctacagGGAGAGCCCCTGTGTGTGTTCTATTCACGTTACGGCATATGCAAATTTGGTCCAAGTTGCAAGTTTGATCACCCAATGGGAGTCTTCACCTATAACATAT

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA10G31370.2 (Glycine max), 3'ss of exon 5
-----------------gtaagctaataaaagacttcagattctttcctttatagtctcatta-tgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
                  |    |  | |      |  | |  | |   || |  |   |||| ||   | || || |  |  ||  |   |||   ||||||||||||  |||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| ||||| |||  | | ||| || | || | | 
acaaatatttgtgttttttttttttttcacgttagtttggtcttgtgagttgtgattgaattagtgcaatctgatagaggca-gtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTCATAATATCT

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA20G36140.1 (Glycine max), 3'ss of exon 6
-------------gtaagctaataaaagacttcagatt----ctttcctttatagtctcatta-tgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
             ||    |        || | |||||     | |   || |  |   |||| ||   | || || |  |  ||  |   |||   ||||||||||||  |||| || ||||||||||| ||||| || ||||| ||||| ||||| || || ||||| ||||| |||  | | ||| ||||||| | ||
caaatatttgtgggttttttttctcttcacgttagattggtcttgtgtgttgtgattgaattagtgcaatctgatagaggca-gtgtcccatttcttacagGGAGAACCTTTGTGTGTCTTCTATTCTCGTTATGGCATATGCAAATTTGGCCCAAGTTGCAAGTTTGACCACCCAATGGAAATTTTCTCTTACAATATCA

upper sequence: AT5G16540.3 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv04s0023g00370.t01 (Vitis vinifera), 3'ss of exon 6
---gtaagctaataaaagacttcagattc--tttcctt--tatagtctcattatgtggtt--tggtaaatt--------cttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
    |||   |  ||   ||||||  ||   || |  |  |||||  || || | | |||  |  ||||||        || |||  |  |||  |||||||||||||  ||||| | || |||||||| |||||||||||||| ||||||||||| || || ||||| ||||| ||| || ||||| | |||||     
accataatgcataaatgtacttcaactttggttgctctgatatagagtccttgtctagttatttataaatttgatggatctggtttttatttttcaacagGGAGAACCTTTGTGCATTTTTTATTCTCGTTATGGGATCTGCAAATTTGGTCCAAGTTGCAAGTTTGACCACCCTATGGGAATCTTCGCATACAATCTGT

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|86083930|gb|DR379689.1|DR379689
EST:     CCCCTCCTCCTGATTGTGTCTTAAGCTCGGTTGGCCTTCCTTTACGCCCG                         GGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGT
genomic: CCCCTCCTCCTGATTGTGTCTTAAGCTCGGTTGGCCTTCCTTTACGCCCGgtaagctaat ... tttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA
                            taaattctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagctaataaaagacttcagattctttcctttatagtctcattatgtggtttggtaaattcttgttgctggtttgaaacagGGAGAACCACTGTGCGTGTTCTATTCTCGGTATGGGATCTGCAAGTTTGGTCCAAGCTGTAAATTTGATCACCCGATGCGAGTCTTCACTTACAACAACA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG