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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaatctcctttctctctttactgcgaaggcttttctaatatttgattgaaatgtaaaaaaacctaaatgagattttaacctatgatcgatgcagGCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGCTGAAGATCTTGAAAGATTGTTGGGTGAGTTGTTTGAAGGAAAGTCTATG

Basic information

species Arabidopsis thaliana
transcript AT5G03540.1
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G03540.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: GLYMA20G33590.1 (Glycine max), 3'ss of exon 11
gtaaaaatctcctttctctctttactgcgaaggcttttctaatatttgattgaaatgtaaaaaaacc-taaatg---agattttaacctatgatcgatgcagGCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGCTGAAGATCTTGAAAGATTGTTGGGTGAGTTGTTTGAAGGAAAGTCTATG
  ||     |  ||  | | ||| |     | || ||     | |||   |||| | |       |  | | ||   |  |   |||||    | | | ||||||| | || |||||||| |||||||||||||| ||||| || ||  |||| |||||||| ||  || |||||||||| || |||||||||||    |||
-caattcattttttgttatgtttgcatttgatgccttgtggttttttatgtgaactattgccttgcaatgagtgcataactgggaacctgctgt-gttacagGCCTCTAGTGGAGAGTGGAAAGAATCCTCAGAAGTACATCAAATACTCAGCAGAAGATCTAGACCGAATGTTGGGTGAATTTTTTGAAGGAAAAAACATG

upper sequence: AT5G03540.1 (Arabidopsis thaliana), 3'ss of exon 11
lower sequence: Vv13s0073g00170.t01 (Vitis vinifera), 3'ss of exon 11
gtaaaaatctcctttctctctttactgcg-aaggcttttctaatatttgattgaaatgtaaaa----aaacctaaatgagattttaacctatgatcgatg-cagGCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGCTGAAGATCTTGAAAGATTGTTGGGTGAGTTGTTTGAAGGAAAGTCTATG
     ||| || || |  |      | |  | |||   |    ||  |  ||  |    |  |    ||| ||  ||  | ||      | || || ||| ||||||  |||||||||||||||||||||| ||||| |||||    |  ||||| || ||||| ||| |  || ||||||| || ||||| || |   |  ||
---gtaatttcattcccattgaatgtccatagggccccttgtttacctagttagacctcatgattctaaagctgcatttgtttcctgttt-tgttcaatggcagGCCACTGGTTGAGAGTGGGAAGAATCCCCAGAAGTACATTCGATTCACAGCAGAGGATCTGGAACGGATGCTGGGTGAATTTTTTGAGGGTAGAACCTTG
















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|124947015|gb|EL022886.1|EL022886
EST:     GTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGG                         GCCTTTGGTTGAGAGTGGGAAGAAT
genomic: GTTGCTGAAGTATTATTGCCTGCTTATAGATCATTCCTCAAACGCTTTGGgtaaaaatct ... atcgatgcagGCCTTTGGTTGAGAGTGGGAAGAAT
EST: gi|124813810|gb|EH898676.1|EH898676
EST:     TTCCTCAAACGCTTTGG                         GCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGC
genomic: TTCCTCAAACGCTTTGGgtaaaaatct ... atcgatgcagGCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atttgattgaaatgtaaaaaaacctaaatgagattttaacctatgatcgatgcagGCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGCTGAAGATCTTGAAAGATTGTTGGGTGAGTTGTTTGAAGGAAAGTCTATG
                                 ttttaac  putative branch site (score: 2)
     attgaaatgtaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaaatctcctttctctctttactgcgaaggcttttctaatatttgattgaaatgtaaaaaaacctaaatgagattttaacctatgatcgatgcagGCCTTTGGTTGAGAGTGGGAAGAATCCTCAGAAATACATAAAGTATACAGCTGAAGATCTTGAAAGATTGTTGGGTGAGTTGTTTGAAGGAAAGTCTATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA