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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttttgatctgaatatggcacattaattggtgtagtagagttagatcattgatgctatttcattttacaagagcaaagtgtttgactttgaaaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG

Basic information

species Arabidopsis thaliana
transcript AT5G23300.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G23300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA10G43220.1 (Glycine max), 3'ss of exon 1
-ttttgatctgaatatggcacattaattggtgtagtagagttagatcattgatgctatttcattttacaagagcaaagtgt-ttgactttgaaaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG
  ||||   ||  | ||    | |   | |  |    | ||  |    |||   || ||  |||||         |  |   |||| |      | ||  |||||||| | ||||||||||| ||||| |||||    |||||||| ||||||||||| |||||||  |||||||| || |||||
tgtttgcattg--tgtgattaagtttgtagcttgcatgtgtatgtatgttgtaacttttatattttgtgtagtttacctacattgattactttgaattgcagGGAAGGTTGTTGACAGGAGCCACCATAGGTCTACTTATAGCTGGTGGAGCTTATGTGAGTACTGTGGATGAAGCTACTTTCTG

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA20G23670.1 (Glycine max), 3'ss of exon 1
ttttgatctgaatatggcacattaattggtgtagtagagttagatcattgatgctatttcattttacaagagcaaagtgt-----ttgactttgaaaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG
     || |   | | |      | || ||    || |  |  ||    | ||  | || || || |  | | |           |||| |     || ||  |||||||| | ||||| ||||| ||||| |||||    |||||||| ||||||||||| |||||||  |||||||| || |||||
-----atatttgtgttgtgatcaagtttgtagcttacatgtgcatgtaggttgtaactttatcttgcttgtgtagttgacctacattgattactttaaattgcagGGAAGGTTGTTGACGGGAGCCACCATAGGTCTACTTATAGCTGGTGGAGCTTATGTGAGTACTGTGGATGAAGCTACTTTCTG

upper sequence: AT5G23300.1 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: Vv10s0042g00140.t01 (Vitis vinifera), 3'ss of exon 1
------ttttgatctgaatatggcacattaattggtgtagtagagttagatcat-tgatgctatttcattttacaagagcaaagtgtttgactttgaaaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG
      ||||    | | | |||  |  |  ||     |  ||   ||   ||| || ||  || |  ||| |        || || |     |||||    |  |||| ||| |||| ||||||||| | ||||| ||   |||||| |||||||||||||| ||||| |  ||||||||||| |||||
ccttttttttttgtttagtttggggcgatgtttaaaacaccagtaatactacatgtgctggaatctggtttgattg----taaatgctgtttcttgaa---ctgcagGGGAGGTTATTCACAGGAGCTGCTATTGGCCTACTCATAGCAGGAGGAGCTTATGTGAGTACCGTGGATGAAGCAACTTTCTG

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|86073993|gb|DR369750.1|DR369750
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
EST: gi|19875233|gb|AU236064.1|AU236064
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACNGGAGCTACCATTGGTCTGGCCNTAGCCTGGAGGAGC
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGC-TGGAGGAGC
EST: gi|86073991|gb|DR369748.1|DR369748
EST:     GGTTCCTGGAGCTTCTTCTGCACCCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: GGTTCCTGGAGCTTCTTCTGCACC-GAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
EST: gi|86073994|gb|DR369751.1|DR369751
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
EST: gi|86070492|gb|DR366249.1|DR366249
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
EST: gi|116483519|gb|EG526111.1|EG526111
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
EST: gi|86073990|gb|DR369747.1|DR369747
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
EST: gi|86073995|gb|DR369752.1|DR369752
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGACA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
EST: gi|86073992|gb|DR369749.1|DR369749
EST:     CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGA                         GGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT
genomic: CGGTTCCTGGAGCTTCTTCTGCACCGAAAGTCCCTCATTTTTCCAAGAGAgtgagtagct ... aaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgatgctatttcattttacaagagcaaagtgtttgactttgaaaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG
                                 gtttgac  putative branch site (score: 4)
                                      actttgaaaatttata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttgatctgaatatggcacattaattggtgtagtagagttagatcattgatgctatttcattttacaagagcaaagtgtttgactttgaaaatttatagGGAAGGATATTGACAGGAGCTACCATTGGTCTGGCCATAGCTGGAGGAGCTTATGTTAGTACTGCAGATGAAGCAACCTTCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acaagag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgtttga