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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TAACTTGCAGCAGGATAAGGACATTGAGTATTGGGGAATCGATTTGGATTCCATTGTTAGAAGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCTgtaaggaacgtttcttgcttttgcaacctgttgaatcatatgaatctgagcatttatcagttggggttttgttgtttacaaatctgttag

Basic information

species Arabidopsis thaliana
transcript AT3G10940.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G10940.1 (Arabidopsis thaliana), 5'ss of exon 2
lower sequence: Vv13s0067g02510.t01 (Vitis vinifera), 5'ss of exon 2
TAACTTGCAGCAGGATAAGGACATTGAGTATTGGGGAATCGATTTGGATTCCATTGTTAGAAGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCTgtaaggaacgtttcttgcttttgca------acctgttgaatcatatgaatctgagcatttatcagttggggtttt--gttgtttacaaatctgttag--
 ||  |||||||||| |||||  ||||||||||||   | || ||    || ||  | | ||||||||| || |||| ||||||||||||||||||||| |||||  |   | |||  |||| ||      |     | ||  | || |||   |   |  |||||  | | | |    || |||  ||   | ||    
AAATCTGCAGCAGGACAAGGATGTTGAGTATTGGGAGGTTGACTTACCATCTATAATAAAAAGATGTAAAGAACTTGAAATCCGTCACATGAGAAGGCCAgtaagagaatctcctttttttttcactaatcattaaataaacaacatcaattcaaaactgaatcagaggagatatctaattcttttgaacaatattttct
















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|47829087|gb|CK118771.1|CK118771
EST:     GAAGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCT                         GCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT
genomic: GAAGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCTgtaaggaacg ... aatctgttagGCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT
EST: gi|47828618|gb|CK118302.1|CK118302
EST:     CCATTGTTAGAAGATGTAAGGAGCTCGTAATCCGTCACATGAGAAGGCCT                         GCTAAAGATCTTGATCC
genomic: CCATTGTTAGAAGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCTgtaaggaacg ... aatctgttagGCTAAAGATTTTGATCC
EST: gi|125199247|gb|EL214201.1|EL214201
EST:     AGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCT                         GCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT
genomic: AGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCTgtaaggaacg ... aatctgttagGCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT
EST: gi|124881966|gb|EH960868.1|EH960868
EST:     AATCCGTCACATGAGAAGGCCT                         GCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT
genomic: AATCCGTCACATGAGAAGGCCTgtaaggaacg ... aatctgttagGCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT
EST: gi|86074744|gb|DR370501.1|DR370501
EST:     CGTCACATGAGAAGGCCT                         GCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT
genomic: CGTCACATGAGAAGGCCTgtaaggaacg ... aatctgttagGCTAAAGATTTTGATCCACTTTCGTTGAGAAGCCAACTTCCAAAAGCTGTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TAACTTGCAGCAGGATAAGGACATTGAGTATTGGGGAATCGATTTGGATTCCATTGTTAGAAGATGTAAGGAGCTTGGAATCCGTCACATGAGAAGGCCTgtaaggaacgtttcttgcttttgcaacctgttgaatcatatgaatctgagcatttatcagttggggttttgttgtttacaaatctgttag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT