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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcttttggggttctgatttagttcatgatagcgtttcatattagctggcatcataacaaagattttttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCCTGTTGTAGCTGCATATGTTTATCGAAG

Basic information

species Arabidopsis thaliana
transcript AT2G44350.2
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G44350.2 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 10
-----gtatgcttttggggttctgatt-tagttcatgatagcgtttcatattagctggcatcataacaaagattttttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCCTGTTGTAGCTGCATATGTTTATCGAAG
      |    |||||  ||  || ||  |   | ||||    | |||  |  ||  ||| | |||    |||  | | || ||||| |||||||||||||||||||||||  || |   |||||||||  || || ||||||||||| ||||||||||||||
gtaggattcttttttgcagtcatgtttacacaacttgattatctatcaattatgcaagca-cttaaatgtgatgatgt-tttcagGTACTGGGAGCCAACATATGAGGATTCTCTTAGTTTGATTGCTCAAGTACCAGTTGTAGCTGCTTATGTTTATCGAAG
















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|116471055|gb|EG513647.1|EG513647
EST:     GTGCAAAGTGAGTTTCAAAAGGCATATGAGAATGGAATTCATAAGTCAAA                         GTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
genomic: GTGCAAAGTGAGTTTCAAAAGGCATATGAGAATGGAATTCATAAGTCAAAgtatgctttt ... tttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
EST: gi|124846936|gb|EH931373.1|EH931373
EST:     ATATGAGAATGGAATTCATAAGTCAAA                         GTTCTGGGAGCCAAACATATGAGGATTGCCTCAA
genomic: ATATGAGAATGGAATTCATAAGTCAAAgtatgctttt ... tttcttccagGTTCTGGGAGCCAA-CATATGAGGATTGCCTCAA
EST: gi|164013831|gb|ES206407.1|ES206407
EST:     AAGGCATATGAGAATGGAATTCATAAGTCAAA                         GTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
genomic: AAGGCATATGAGAATGGAATTCATAAGTCAAAgtatgctttt ... tttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
EST: gi|47832067|gb|CK121751.1|CK121751
EST:     GTGCAAAGTGAGTTTCAAAAGGCATATGAGAATGGAATTCATAAGTCAAA                         GTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
genomic: GTGCAAAGTGAGTTTCAAAAGGCATATGAGAATGGAATTCATAAGTCAAAgtatgctttt ... tttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
EST: gi|116453292|gb|EG495884.1|EG495884
EST:     GTGCAAAGTGAGTTTCAAAAGGCATATGAGAATGGAATTCATAAGTCAAA                         GTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
genomic: GTGCAAAGTGAGTTTCAAAAGGCATATGAGAATGGAATTCATAAGTCAAAgtatgctttt ... tttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
EST: gi|164217132|gb|ES133792.1|ES133792
EST:     TGGAATTCATAAGTCAAA                         GTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
genomic: TGGAATTCATAAGTCAAAgtatgctttt ... tttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
EST: gi|301502837|gb|HO208377.1|HO208377
EST:     ATTCATAAGTCAAA                         GTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC
genomic: ATTCATAAGTCAAAgtatgctttt ... tttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttcatgatagcgtttcatattagctggcatcataacaaagattttttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCCTGTTGTAGCTGCATATGTTTATCGAAG
                              tcataac  putative branch site (score: 2)
                                          ttttttcttcc  putative PPT
                                ataacaaagatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatgcttttggggttctgatttagttcatgatagcgtttcatattagctggcatcataacaaagattttttcttccagGTTCTGGGAGCCAACATATGAGGATTGCCTCAACCTGATTGCTCGTGTTCCTGTTGTAGCTGCATATGTTTATCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC