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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA

Basic information

species Arabidopsis thaliana
transcript AT4G04040.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA09G01050.1 (Glycine max), 3'ss of exon 10
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacc-tgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA
   ||| |         | |     ||         || |     |    |||| | | || |  ||  |  | |  |||| || |||  ||| |||       | |  || ||||||| || ||||| |||||||||||| | ||||||||||||||||| ||| | ||||| |  |||  ||| || | |||  || |||| || |  ||| 
--gtgcctaatgttgttattgtgctatcttgctgggttgat---ttggctcctctatccaatttaaatcggcacctatgttaatcttg--cctgtat-------tcccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAAAGGCGAATTTAAAGGGC

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA07G39380.2 (Glycine max), 3'ss of exon 10
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA
                   |   | ||  |    | ||  |    |      |  | |   |  | | || ||      | |   | ||  ||  |||  |||| |  || ||||||| || ||||| |||||||||||| | ||||||||||||||||| ||| | ||||| |  |||  | |||| |||||| || | |  || | |||| 
------------------gtgcttaatgtattatagttctatacttgctgtgtttatcttgcctgtaatgcaatttgactaagcctcaatgttggtatatatttccattt-agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCACATATAAAGGAGGATTTAGGGGGC

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA17G01360.1 (Glycine max), 3'ss of exon 8
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA
                        |     ||   |||| |  |||| | | | |      |  | | || ||      | |   | ||  ||  |||  |||| |  || ||||||| || ||||| |||||||||||| | ||||||||||||||||| ||| | ||||| |  |||  | ||||  ||||| || |||  || | |||| 
------------------------gtgcttaatgtattatagtgctata-ctttatcttgccctgtaatgcaatttgactaagcctcaatgttggtatatatttccattt-agGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAACAGGGCTCATATAAAGGCGGATTTAGGGGGC

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G11890.1 (Glycine max), 3'ss of exon 10
--gtctgcttctatc-caccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacc-tgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA
  | ||  |  | |   |   ||| ||   |      | ||    ||||    |||| | | || | |||  |  | |  |||| || |||     || |||     | |  || ||||||| || ||||| |||||||||||| | ||||||||||||||||| ||| | ||||| |  |||  ||| || | |||  |  |||| || |  ||| 
gtgcctaatgttgttatagtgctatcttgctgtgtttattt----ggct----cctctatccaatttgaagcggcaccaatgttaatcttg----cttgtat-----tgccatttagGTTGCCAAGATAGAAACAGAGAAAATGCTTATTCAAATGGTTGAAACTGAGTTGGAGAAGAGAAAGCAAGAAGGCAAATACAATGGCGAATTTAAAGGGC

upper sequence: AT4G04040.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv10s0116g00360.t01 (Vitis vinifera), 3'ss of exon 10
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGA-GTTCATGGGGA
    |  | ||||    |    ||  |  |      |       ||  |       | ||    ||  |  |    || |||||   || ||      |  |||   | | ||||||| |||||||| |||||||||||| | || |||||||||||||||||| ||||||| | |||||  ||||| |||||  ||  | | | |||      
----gtgtttatcttatat--gctagtatatgtgtgtatttgaactttacttgtttgtaattctga--tagatctttggttattgataatct------gtttttataccttagGTTGCAAAAATAGAAACAGAGAAAATGCTTATACAAATGGTTGAAACCGAGTTAGAGAAGAGGAAGAGTGAGGGCACATACAAATACAAAGGTCACTTTA-

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|124813817|gb|EH898683.1|EH898683
EST:     CTATTCAAGAACAACTAATGCTTGAGAGAGATCCACATGGAAATGTGCAG                         GTTGCTAAAATA
genomic: CTATTCAAGAACAACTAATGCTTGAGAGAGATCCACATGGAAATGTGCAGgtctgcttct ... ttctcttcagGTTGCTAAAATA
EST: gi|124891488|gb|EH970390.1|EH970390
EST:     TGGAAATGTGCAG                         GTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAG
genomic: TGGAAATGTGCAGgtctgcttct ... ttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA
                                           ttttctcttc  CT-rich tract
                    tttattttgaaccttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtctgcttctatccaccactaactgattcaaacaaattaaaaggctaaaacctcaagcaaactcgaactgaaaacctgtttattttgaacctttatatgaattttctcttcagGTTGCTAAAATAGAGACAGAGAAAATGTTGATTCAAATGGTTGAAACCGAGCTAGAGAAAAAGAAGACAGAGGGTACATATGAACGCGAGTTCATGGGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG