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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctaatctttagatttggattcgtttttgtgttatgcatattttgttttctggtttatgattagtggaaggtgagattaacaagtagggcagtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTCTCTAATATCTTACGAGCTGGAGGATATTCTGTTGGTTGTTATTCTAG

Basic information

species Arabidopsis thaliana
transcript AT5G41480.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G41480.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G07590.1 (Glycine max), 3'ss of exon 2
-ctaatctttagatttggatt---cgtttttgtgttatgcatattttgtt--ttctggtttatgattagtggaaggtgagattaacaagtagggcagtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTCTCTAATATCTTACGAGCTGGAGGATATTCTGTTGGTTGTTATTCTAG
    |  || | ||  | |||    | ||  |  ||| | || ||||  |  ||   ||| ||  |  || |  | ||  | |    | |         ||| |||| ||||||| |||||||||||||||| || ||||||||  |||||||| | ||||||||  |  |   || ||| |||||||||||||||||  | ||
atggaagttaaaatgggcattttatgcttgggctttagggatgtttttgtactttcagttgattttatgtagttgatggaagtgctcactc------caattgtagGCTGTTCATATTGCTGGAACTAAGGGGAAGGGATCAACAGCTGCTTTTGTATCTAATATTCTGAGGAATGAAGGCTATTCTGTTGGTTGTTACACCAG

upper sequence: AT5G41480.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA14G31620.1 (Glycine max), 3'ss of exon 2
-ctaatctttagatttggatt---cgtttttgtgttatgcatattttgtt--ttctggtttatgattagtggaaggtgagattaacaagtagggcagtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTCTCTAATATCTTACGAGCTGGAGGATATTCTGTTGGTTGTTATTCTAG
    |  || | ||  | |||    | ||  |  ||| | || ||||  |  ||   ||| ||  |  || |  | ||  | |    | |         ||| |||| ||||||| |||||||||||||||| || | ||||||  |||||||| | ||||||||  |  |   || ||| |||||||||||||||||  ||||
atggaagttaaaatgggcattttatgcttgggctttagggatgtttttgtactttcagttgattttatgtagttgatggaagtgctcactc------caattctagGCTGTTCATATTGCTGGAACTAAGGGGAAGGCATCAACAGCTGCTTTTGTATCTAATATTCTGAGGAATGAAGGTTATTCTGTTGGTTGTTACACTAG

upper sequence: AT5G41480.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv16s0050g02490.t01 (Vitis vinifera), 3'ss of exon 2
-----ctaatctttagatttggattcgtttttgtgttatgcatattttgttttctggtttatgattagtggaaggtgagattaacaagtagggcagtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTCTCTAATATCTTACGAGCTGGAGGATATTCTGTTGGTTGTTATTCTAG
       |||  ||  |||    | ||  | ||   ||      ||   |||||   |||||  | |||   |  | || ||||  |||    |||  |||||||| ||||||  ||||||| || || |||||||| |||||| |||| |||||  | ||||| |||||  | | ||| ||| |||||||||||||| ||||
atcagtgaatggttgcattgcattgcgaatatgcactacat---ttgaattttcatatttatt-tgagtatgaatttag-ttaattagtgtaacagcaattatagGCTGTTCACATTGCTGGGACCAAAGGAAAAGGGTCAACTGCTGCATTTCTTGCCAATATTTTACGGACAGAAGGTTATGCTGTTGGTTGTTATACTAG

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|116485042|gb|EG527634.1|EG527634
EST:     GAATGAAACGTCTCATGCTTCGCCTCCGTAATCCTCATTACAAATACAAG                         GTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTC
genomic: GAATGAAACGTCTCATGCTTCGCCTCCGTAATCCTCATTACAAATACAAGgttcgtgctt ... gtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTC
EST: gi|116485040|gb|EG527632.1|EG527632
EST:     GAATGAAACGTCTCATGCTTCGCCTCCGTAATCCTCATTACAAATACAAG                         GTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTC
genomic: GAATGAAACGTCTCATGCTTCGCCTCCGTAATCCTCATTACAAATACAAGgttcgtgctt ... gtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctggtttatgattagtggaaggtgagattaacaagtagggcagtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTCTCTAATATCTTACGAGCTGGAGGATATTCTGTTGGTTGTTATTCTAG
                            gattaac  putative branch site (score: 2)
       tttatgatta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctaatctttagatttggattcgtttttgtgttatgcatattttgttttctggtttatgattagtggaaggtgagattaacaagtagggcagtgattatagGTTGTTCATGTTGCTGGAACTAAGGGAAAAGGATCAACTTCTGCTTTTCTCTCTAATATCTTACGAGCTGGAGGATATTCTGTTGGTTGTTATTCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - gatttgg
- - - - - - - - - - -gtttttg
- - - - - - - - - - - - - - - - - - - - - - - - - ggtttat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taacaag