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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaatataaaaaacttaaatctgatagcttcttgcaaacatattgctttggaatctttttactgtttgtgtcatttcttatccattgtcttggtgtttttgctgggtactgattttttgcatcgtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTTGTTAGGCAATCCAACTTCAAGCTTCCTTCTGATTCTAAGGTACCGATCA

Basic information

species Arabidopsis thaliana
transcript AT4G30210.1
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G30210.1 (Arabidopsis thaliana), 3'ss of exon 13
lower sequence: Vv11s0052g00880.t01 (Vitis vinifera), 3'ss of exon 13
gtaaatataaaaaacttaaatctgatagcttcttgcaaacatattgctttggaatctttttactgtttgtgtcatttcttatccat-tgtcttggtgtttttgctgggtactgattttttgcatcgtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTTGTTAGGCAATCCAACTTCAAGCTTCCTTCTGATTCTAAGGTACCGATCA
                                ||| | ||    || ||  |  |  | |  |  | | | |||| ||| |   || ||   |     |||   |   ||   | ||     ||  |  || ||| |||||||||| |  ||| | ||  || | ||   || |||||| || ||||||||||||||||||||||| |||||| ||||| ||   || ||||| |
-------------------------------attgaacactgtctggttcag--ttatatggccatatctctcatgtctcagatatgtggactttaactttccttttctaaaaacttcc--aatttttttcgcagTATGCTGTGCCCTTGGAGGAAAGCCAAGATTGCAGCTGGGCGCCAATTTTTGTTAGGCAATCCAACTTCAAACTTCCTGCTGATACTTCAGTGCCGATTA
















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|116436419|gb|EG479011.1|EG479011
EST:     AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAG                         AATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
genomic: AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAGgtaaatataa ... gtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
EST: gi|86044356|gb|DR340111.1|DR340111
EST:     AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAA                         AATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
genomic: AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAGgtaaatataa ... gtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
EST: gi|86044357|gb|DR340112.1|DR340112
EST:     AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAG                         AATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
genomic: AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAGgtaaatataa ... gtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
EST: gi|86044360|gb|DR340115.1|DR340115
EST:     AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAG                         AATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
genomic: AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAGgtaaatataa ... gtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
EST: gi|86044358|gb|DR340113.1|DR340113
EST:     AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAG                         AATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT
genomic: AAATGCCAACTGGCAGGATTCATAAGGGAGTGTGTTCCACTTGGATGAAGgtaaatataa ... gtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatccattgtcttggtgtttttgctgggtactgattttttgcatcgtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTTGTTAGGCAATCCAACTTCAAGCTTCCTTCTGATTCTAAGGTACCGATCA
                            tactgat  putative branch site (score: 2)
                               tgatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaatataaaaaacttaaatctgatagcttcttgcaaacatattgctttggaatctttttactgtttgtgtcatttcttatccattgtcttggtgtttttgctgggtactgattttttgcatcgtaatcacagAATGCTGTGCCTTACGAGAAGAGTGAAAACTGTTCCTCGGCGCCGATATTTGTTAGGCAATCCAACTTCAAGCTTCCTTCTGATTCTAAGGTACCGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT