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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cggataataatctttatgtactcttttgggtagcatcgtaatggttattacaatgtaaaattgctacagctaatcttaccaaaactttatgctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCATGTTCTCTTCAAG

Basic information

species Arabidopsis thaliana
transcript AT1G09330.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G09330.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: LOC_Os01g22870.1 (Oryza sativa), 3'ss of exon 1
-cggataataatctttatgtactcttttgggtagcatcgtaatggttattacaatgtaaaattgctacagctaatcttaccaaaactttatgctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCATGTTCTCTTCAAG
   ||    | |  | |     |||| |   |  |   |        |||   || ||  | ||  |          ||   |   | |||| ||   | | | ||||     |  || ||||||||||| |||| ||||||| | |||||||| |||||||||
cttgactgcactaataactatttcttctcaattcctctgctgcttaaattgagatttaggagtggcatga-------tagtgatgatatatgtttctgttgctgcagGTGGTCGGCGAGAATTATGCAAATCCAAAGACATGTTTCTTCCATGTCCTCTTCAAG
















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|86026654|gb|DR322407.1|DR322407
EST:     TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
EST: gi|86026658|gb|DR322411.1|DR322411
EST:     TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
EST: gi|86026656|gb|DR322409.1|DR322409
EST:     TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
EST: gi|86026659|gb|DR322412.1|DR322412
EST:     DVTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: -CTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
EST: gi|86026657|gb|DR322410.1|DR322410
EST:     TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACSCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
EST: gi|19875328|gb|AU236159.1|AU236159
EST:     TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
EST: gi|86026655|gb|DR322408.1|DR322408
EST:     TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
EST: gi|116471900|gb|EG514492.1|EG514492
EST:     TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAG                         ATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT
genomic: TCTCGGATTGATCCTTTTGGATTCTTCGAAAGATGGACCCTAATAATCAGgtgaattttc ... gctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattacaatgtaaaattgctacagctaatcttaccaaaactttatgctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCATGTTCTCTTCAAG
                           atcttac  putative branch site (score: 3)
                                       ctttatgctttctt  putative PPT
      aatgtaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cggataataatctttatgtactcttttgggtagcatcgtaatggttattacaatgtaaaattgctacagctaatcttaccaaaactttatgctttcttagATACAGGCACCAGTTGAAAATTATGCAAACCCAAGGACATGTCTTTTCCATGTTCTCTTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaactt