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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG

Basic information

species Arabidopsis thaliana
transcript AT5G10490.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G02840.1 (Glycine max), 3'ss of exon 9
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcct----gttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
                                     |    ||  |   ||   | || || |  |  |||||    ||||  ||   || || ||        ||    |    ||   |  | |  || ||||| || |||||||| ||||||||||| ||||||||||||||||| || |||||  | ||||| ||||||||||||||||| ||||| ||||| || ||||
-----------------------------------gtgtgggatttatcattgcttctaaacataacaattccttgtagtttagtggccaaaatgttattgtggcacctgttgacattcaatgatattttttcagATATTTACAAACTTCCTTTCAAGTGTGATGATTCATGCAACCCGACCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG

upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G33170.1 (Glycine max), 3'ss of exon 9
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcc----tgtttta-tgctaaagatatt-tcataaaaactga-gtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
                                     |    ||  |   ||   | || || |  |  |||     | ||||| ||   || || || |  |   | |||  | | ||   || | |||| ||  |||| || |||||||| ||||| ||||| |||||||||||||||||||| |||||  | ||||| ||||||||||||||||| ||||| ||||| || ||||
-----------------------------------gtgtgggatttatcattgcttctaaacatcacagttcacttgtattttagtggccaaaatgttattgtggcacctgttgatgttaaatgatatttgttt--agATATTTACAAACTTCCTTTCGAGTGTGATGATTCATGCAACCCGGCCTTTTGTGGTTAATGAATGGATTCAAACAAAGATTGAAGGATATGAGGTTTCTG

upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: Vv00s0313g00020.t01 (Vitis vinifera), 3'ss of exon 9
--------------gtgaaacctaattctcattttaat-------tactggtttcttcggaatatccactgt-tagctttagac--gttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
               |  |||  | | ||  || | |        |  ||||||    | |    | | | | |  |||| | |  ||||| | | | | | |       |  |||||||  ||  ||||   |||||||| || |    ||||||| || ||||| || || |||||||  ||||| |||||||| ||||| |||||| ||||||| ||||||||||| |  || ||||| |||||||| ||||
gtgcaaatttgtccatttaacacactgctatttatgaaacacacattttggttttcctgcatgcccaattatgtttcttttgccttgttccctcttcagatatggatcttacttatttca--aagcctga---tttttttgcttatcatatccagATATTCACAAATTTCCTCTCAAGTGCAATGATCCATGCAACTCGGCCTTTTGTTGTGAATGAATGGATTCAAACCAGAATTGAAGGCTATGAAGTTTCTG

upper sequence: AT5G10490.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ18544 (Selaginella moellendorffii), 3'ss of exon 5
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
                                                 ||||| ||   ||||||   || ||||||| | | ||| | ||  ||  |             |||| | |||||     ||||||| || |||||| | || ||||||||||||||||| |||||||| ||||||  | | |||||||| ||||| || || || ||  | ||||| ||||
-------------------------------------------------gttagatt---acgttctcctttctgttttcttcaaaacaaatgacagga-------------ttttatgttttg----tagATTTTTACGAACTTTTTGTCCAGTGTTATGATTCATGCTACCCGGCCGTTTGTTGAGTACGAGTGGATACAAACTAAAATCGATGGGCAGGAAGTTTCTG

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|125066043|gb|EL133055.1|EL133055
EST:     TGCTGGAGGTCTTGGGACAGTTTTGATTACTCTTGCTGGCCGAGAG                         ATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTT
genomic: TGCTGGAGGTCTTGGGACAGTTTTGATTACTCTTGCTGGCCGAGAGgtgaaaccta ... ttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG
    tgctaaa  putative branch site (score: 2)
                               tttttttttgtttttt  putative PPT
            atatttcataaaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaacctaattctcattttaattactggtttcttcggaatatccactgttagctttagacgttccttttcctgttttatgctaaagatatttcataaaaactgagtttttttttgttttttggttccagATTTTGACAAACTTTCTTTCAAGTGTTATGATTCATGCAACCCGGCCATTTGTTTTGAATGAGTGGATTCAAACAAAGATAGAAGGTTATGAAGTGTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA