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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcaactggtctcttatatacaacttacattcagccttggaaacttaaatcatttcctatgtattaaggctggttttgggacgatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G75380.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G75380.3 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G07830.1 (Glycine max), 3'ss of exon 6
gtctgcaactggtctcttatatacaacttacattcagccttggaaacttaaatcatttcctatgtattaaggctggttttgggacgatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG
|  || |  | ||    |   |    |   ||  ||          |   ||   ||   | ||||| |  | |    ||       |  |  |||| || |||| | | || | ||| |||||||||||| | ||||||||||| |||||||| || || |||||||||
gcatgtactttgtacacttcctc--gcccccacccaaaaaaaaggcccccaagtgttgtat-tgtataacagttaaaattatatt--tggtatagGTTGGAAATGACGCAGAATATGTGAGCTTTGATCTTCGACCTTCAGATGCTATCAATATTGCAGTAAGATGCAAG
















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|124988151|gb|EL060557.1|EL060557
EST:     GCATATTTTGCCCAGTTATTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA
genomic: GCATATTTTGCCCAGTTATTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA
EST: gi|125211830|gb|EL226784.1|EL226784
EST:     GTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGG
genomic: GTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGG
EST: gi|124977976|gb|EL051242.1|EL051242
EST:     AGTTCACGAGGCATATTTTGCCCAGTTATTTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA
genomic: AGTTCACGAGGCATATTTTGCCCAGTTA-TTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA
EST: gi|125089298|gb|EL147720.1|EL147720
EST:     CCCAGTTAATTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA
genomic: CCCAGTT-ATTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA
EST: gi|125261697|gb|EL275782.1|EL275782
EST:     TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGG
genomic: TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGG
EST: gi|124955850|gb|EL030827.1|EL030827
EST:     TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAG
genomic: TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAG
EST: gi|125319250|gb|EL333335.1|EL333335
EST:     TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGA
genomic: TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGA
EST: gi|47829045|gb|CK118729.1|CK118729
EST:     TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAG                         GTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA
genomic: TCACCAAAAGAGTTCACGAGGCATATTTTGCCCAGTTATTCCTTTCAAAGgtctgcaact ... gatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggaaacttaaatcatttcctatgtattaaggctggttttgggacgatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG
       ttaaatcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcaactggtctcttatatacaacttacattcagccttggaaacttaaatcatttcctatgtattaaggctggttttgggacgatattgcagGTGGGTAATGCCTCGGAGTGTGTCAGCTTTGATCTTAGGCCTTCAGATGCAATCAATATAGCTGTTAGATGCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT