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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcgagtctaaatctcttgagtattttatattttgaccctctttgatcatctttcacactttactatttccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT

Basic information

species Arabidopsis thaliana
transcript AT4G39520.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G158021_T01 (Zea mays), 3'ss of exon 5
-------------gtaagtcgagtctaaatctcttgagtattttatattttgaccctctttgatcatctttcacactttactatttc----------cagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT
              |   |    |     | |   | ||  ||| | |   || ||  ||          |   |  || ||||||           |||||||| || || ||||||||||||||    || || || ||||||||||||||||||||||| |||||||||||||| ||||| || ||||| |||||||
taacacttcagtcttggattttcttgtgttattccgtgttctttgtgtgcggaaccatttcttcttgggcttgaaagttcctatttttgtggcttgacagGTTATCAGCACAGCTAGGACATGCAATGTTATTTTGATTGTTCTTGATGCCATAAAACCAATAACTCACAAGCGTCTTATTGAGAAGGAGCTTGAAGGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA06G15180.2 (Glycine max), 3'ss of exon 5
------gtaagtcgagtctaaatctcttgagtat--tttatattttgaccctctttgatcatctttcacactt--------tactatttc-------cagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT
        ||  |   | | | | | |      |  || | |     ||   |  ||||    ||||| | ||        || | |||        |||||||| ||||| || ||||||||||| ||||| || || || |||||||| ||||| ||||| |||||||||||||| || ||||||||||| || ||||
aagttcacaatgcacctttcattttttcacacctcattcacacaccaacaaacactgatatattttcataattcatttatatattgttttgcaaacacagGTTATTAGTACTGCAAGGACATGCAATTGCATTTTGATTGTCCTTGATGCAATAAAGCCAATAACTCACAAGCGTCTTATAGAAAAAGAGCTAGAGGGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA04G39690.1 (Glycine max), 3'ss of exon 5
-------gtaagtcgagtctaaatctcttgagtat-tttatattttgaccctctttgatcatctttcacactt--------tactatttc-------cagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT
         ||  |   | | | | ||   | |   || | |     ||   |  ||||    ||||  | ||        || | |||        |||||||| ||||| || || |||||||| ||||| || || || |||||||| || || ||||| ||||| |||||||| || ||||||||||| || ||||
acctttcacaatgcacctttcattttccacacttcattcacacaccaacaaacactgatacattttcgtaattcatttatttattgttttggaaatgcagGTTATTAGTACTGCAAGAACATGCAATTGCATTTTGATTGTCCTTGATGCAATTAAGCCAATAACTCATAAGCGTCTTATCGAAAAAGAGCTAGAGGGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0031g01620.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtaagtcgagtctaaatctcttgagta--ttttatattttgaccctctttgatcatctt-------tcacactttactatt-tccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT
             ||| ||   || |     |  |  | |   || ||||  | | |||  | | |||   |       |  ||  | |  | | |||||||||| || || ||||| |||||||| ||||| || || ||||||||||| ||||| |||||||||||||||||||| || || ||||||||||| ||||
taataatcacttagtatgtaatgtttcttgtttgtatgcaatcttcatatgctcatccttctggctcaatatattaaaatggcatgtcatcaatatccagGTTATCAGCACTGCTAGAACATGCAATTGCATTTTGATTGTTCTTGATGCAATAAAGCCAATTACTCACAAGCGTCTGATAGAGAAAGAGCTCGAGGGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ34569 (Selaginella moellendorffii), 3'ss of exon 4
gtaagtcgagtctaaatctcttgagtattttatattttgaccctctttgatcatctttcacactttactatttccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT
    ||   ||   ||| | ||||| || ||    |      ||  |  |   |||||  |          |  |||||||| ||||| || || || |||||||||||| | |||||||| || || || || || ||||| |||||| | ||||| || ||||||||||||||||
----gtaaggt--gaattttttgagaatattgctatgaagagctactcaaatgtctttgtc---------ctggcagGTTATCAGTACCGCAAGAACTTGCAACTGCATCATCATAGTTCTGGACGCAATCAAGCCCATTACACACAAGAGGCTCATCGAGAAAGAGCTCGAAGGAT

upper sequence: AT4G39520.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: EFJ09453 (Selaginella moellendorffii), 3'ss of exon 5
gtaagtcgagtctaaatctcttgagtattttatattttgaccctctttgatcatctttcacactttactatttccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT--------
    ||   ||   ||| | ||||| || ||    |      || ||  |   |||||  |          |  |||||||| ||||| || || || |||||||||||| | |||||||| || || || || || ||||| |||||| | ||||| || ||||||||||||||||        
----gtaaggt--gaattttttgagaatattgctatgaagagctattcaaatgtctttgtc---------ctggcaggttatcagTACCGCAAGAACTTGCAACTGCATCATCATAGTTCTGGACGCAATCAAGCCCATTACACACAAGAGGCTCATCGAGAAAGAGCTCGAAGGATTTGGAATA

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|47830368|gb|CK120052.1|CK120052
EST:     TTCCTGGTATTATTGAGGGTGCTAAAGATGGAAAAGGTAGAGGAAGACAG                         GTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCC
genomic: TTCCTGGTATTATTGAGGGTGCTAAAGATGGAAAAGGTAGAGGAAGACAGgtaagtcgag ... ctatttccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCC
EST: gi|125072216|gb|EL136986.1|EL136986
EST:     GGTGCTAAAGATGGAAAAGGTAGAGGAAGACAG                         GTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTT
genomic: GGTGCTAAAGATGGAAAAGGTAGAGGAAGACAGgtaagtcgag ... ctatttccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtattttatattttgaccctctttgatcatctttcacactttactatttccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT
                                             ctatttcc  CT-rich tract
     ttttatattttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcgagtctaaatctcttgagtattttatattttgaccctctttgatcatctttcacactttactatttccagGTTATAAGTACGGCTAGGACATGCAACTGCATCTTAATAGTTCTTGATGCCATAAAACCAATTACTCACAAGCGTCTCATTGAAAAAGAGCTCGAAGGAT

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