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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGGTGAGTGGTACAATTCGCTCGCAGATCTGTACCAGAAGAAGCTCTGGCATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctcttgaattttcatcgtttcgtagttcttctgtgtgattagggttcatagatctcgagaaagttaataggagtcgtcatgttagacttgggtt...

Basic information

species Arabidopsis thaliana
transcript AT4G19006.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G19006.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA09G34310.1 (Glycine max), 5'ss of exon 1
TGGTGAGTGGTACAATTCGCTCGCAGATCTGTACCAGAAGAAGCTCTGGCATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctcttgaattttcatcgtttcgtagttcttctgtgtgattagggttcatagatctcgagaaagttaataggagtcgtcatgtta-gacttgggtt--
    || |||||||||||||| || |||||||||||||||||||||||||| ||||||||||| ||||||||||||||  | |||||| | ||||| |||||  | |||||   |  | | |  | || | || || |   || |        ||   |   |     ||   |  |  | ||  ||||   ||    |||  
CTCCGATTGGTACAATTCGCTGGCGGATCTGTACCAGAAGAAGCTCTGGCACCAGCTCACTCTCAAGCTCGAGCAGTTTGTGGCTCTCGCCGTCTTCCAGgttcagctcttctttccttaccact-cgcaattattgttgttgttctataactattattactggcttcgt--gtttgctttgttttgtttcaacgattgttag

upper sequence: AT4G19006.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: GLYMA01G01460.1 (Glycine max), 5'ss of exon 1
TGGTGAGTGGTACAATTCGCTCGCAGATCTGTACCAGAAGAAGCTCTGGCATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctcttgaattttcatcgtttcgtagttcttctgtgtgattagggttcatagatctcgagaaagttaataggagtcgtca-tgttag--acttgggtt-
    || |||||||||||||| || ||||| |||||||| ||||||||||| ||||| || || ||||| ||||||||| | |||||| | ||||| ||||| | |||  ||  ||| | |||| |    | ||||     |    |  |||  |   |||  |     ||  | || || |  | || |    ||| | |   
CTCCGATTGGTACAATTCGCTGGCGGATCTATACCAGAACAAGCTCTGGCACCAGCTTACCCTCAAGCTTGAGCAGTTCGTGGCTCTCGCCGTCTTCCAGgtaactcttctgtctttac-tcgtattaccgctctttccactcccaattgtttgt---tctgaaacttttttgtgggggttggtagtgatgtgcactcgagaga

upper sequence: AT4G19006.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: Vv02s0012g02660.t01 (Vitis vinifera), 5'ss of exon 1
TGGTGAGTGGTACAATTCGCTCGCAGATCTGTACCAGAAGAAGCTCTGGCATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctcttgaattttcatcgtttcgtagttct---tctgtgtgattagggttcatagatctcgagaaagttaataggagtcgtcatgttagacttgggtt
 |  || |||||||| || || |||||||||||||||| |||||||||||| || |||||||| || ||||| |||||| |||||||  | |||||||||| |  |  |   |  ||||  | |||  ||  | |   ||| | |  |    ||   | |          | ||   |    |  |  | ||  | || |   
GGCAGAATGGTACAACTCTCTTGCAGATCTGTACCAGAGGAAGCTCTGGCACCAACTCACTCTCAAACTCGAACAGTTCGTCGCTCTTGCAGTCTTTCAGgcctgttcccccatctttctccattttctatctttaattcttttttttctcagtatgtggtgtggtttggatttcgaattttttattttattttatttag---

upper sequence: AT4G19006.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ05758 (Selaginella moellendorffii), 5'ss of exon 1
------TGGTGAGTGGTACAATTCGCTCGCAGATCTGTACCAGAAGAAGCTCTGGCATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctcttgaattttcatcgtttcgtagttcttctgtgtgattagggttcatagatctcgagaaagttaataggagtcgtcatgttagacttgggtt
      ||  ||||||||||||   || ||  |||| |||| | | |||||||||||||||||||| || ||||||||| | ||| ||   | |    ||      | |||||||| |   | ||      ||   |    | |  ||||  |    |  |     |   |   |||  | | ||                     
GGATCTTGCCGAGTGGTACAATGATCTGGCGCATCTATACCGGCACAAGCTCTGGCATCAGCTCACGCTCAAGCTCGAGAAATTCTTCCAGCACC---TCCGGgtaggcaatctctcgccctctcgctccctctccggagattttggtga--aaatctggtgatattatggtgggttgcttgcag---------------------

upper sequence: AT4G19006.1 (Arabidopsis thaliana), 5'ss of exon 1
lower sequence: EFJ34882 (Selaginella moellendorffii), 5'ss of exon 1
------TGGTGAGTGGTACAATTCGCTCGCAGATCTGTACCAGAAGAAGCTCTGGCATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctcttgaattttcatcgtttcgtagttcttctgtgtgattagggttcatagatctcgaga-aagttaataggagtcgtcatgttagacttgggtt
      ||  ||||||||||||   || ||  |||| |||| | | |||||||||||||||||||| || ||||||||| | ||| ||   | |    ||      | |||||||| |   | |   || | | |    |     | || | |   |     ||| |   |    |||  | | ||                     
GGATCTTGCCGAGTGGTACAATGATCTGGCGCATCTATACCGGCACAAGCTCTGGCATCAGCTCACGCTCAAGCTCGAGAAATTCTTCCAGCACC---TCCGGgtaggcaatctctcgccctct---cgctccctctcccgagattttggtgaaaatctggtgatattatggtgggttgcttgcag---------------------

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|86031853|gb|DR327606.1|DR327606
EST:     ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAG                         GCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
genomic: ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctct ... atctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
EST: gi|86031851|gb|DR327604.1|DR327604
EST:     ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAG                         GCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
genomic: ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctct ... atctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
EST: gi|86031852|gb|DR327605.1|DR327605
EST:     ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAG                         GCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
genomic: ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctct ... atctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
EST: gi|116463707|gb|EG506299.1|EG506299
EST:     ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAG                         GCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
genomic: ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctct ... atctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
EST: gi|19877782|gb|AU238613.1|AU238613
EST:     ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAG                         GCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
genomic: ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctct ... atctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
EST: gi|86031850|gb|DR327603.1|DR327603
EST:     ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAG                         GCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG
genomic: ATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctct ... atctttgcagGCTGGAGATGCTTTAATACAGCTTTACAACAATTTCATCACTGACTTTGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGGTGAGTGGTACAATTCGCTCGCAGATCTGTACCAGAAGAAGCTCTGGCATCAGCTCACTCTTAAGCTCGAGCAGTTCATCGCTCTCTCTGTCTTTCAGgtcaatctcttgaattttcatcgtttcgtagttcttctgtgtgattagggttcatagatctcgagaaagttaataggagtcgtcatgttagacttgggtt

- - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG