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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagtggttcagcattattatgaattcagtgcactgcttattcaatatttctgtttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG

Basic information

species Arabidopsis thaliana
transcript AT4G24190.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G37820.1 (Glycine max), 3'ss of exon 7
---gaagtggttcagcat-tattatgaattcagtgcactgcttattcaatatttctgtttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG
    || |  || |  ||   || |    ||| |   || ||   |||||||    |       |||| |  |   |   | | | ||    | | |   ||||||||||||||||||||| |||||||| ||||||||||||||||   | ||||| ||||||||||||||    ||||| || | ||| |||||||| ||  
ataaaactcatttaatatacgtttttttgtcaatat-ctactc--tcaatatgaaagacgtcaatctcttgctaaatatgatttaacaactatttttttcacaGGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAGGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCC-

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA14G40320.4 (Glycine max), 3'ss of exon 7
gaagtggttcagcattattatgaattcagt---gcactgcttattc--aatatttctgt--ttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG
        ||   |||| |||  |||   |    || |   |||||  |||||    |     | |||||  | ||  |    | | | ||    ||| |   ||||||||||||||||||||| |||||||| ||||||||||||||||   | ||||| |||||||| |||||    ||||| || | ||| |||||||| ||  
-----aaatctcaattaatatacattttttttgtcaatatctattctcaatataaaagaagccaacctcttgt-ataat-atgatttaacaactatgtttttcacagGAATTGGTGAAGAGATACTCTGAATTTATTAACTTCCCTATCTATATTTGGGCAAGCAAAGAAGTTGATGTGGAGGTTCCCGCTGATGAAGATGATTCCA

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv18s0001g14500.t01 (Vitis vinifera), 3'ss of exon 7
gaagtggttcagcattattatgaattcagtgcactgcttattcaatatttctgtttatcc-tctcattatggttgctaatgatcat-tgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG
 |  |  ||     || ||||   | || || | |       || | ||    | ||    |||  ||  ||||  ||||  |  |   |||   | |  |||| || ||||| ||||||||||||||||| ||||| || || | ||||||||| ||||||||||||||    ||||| || |  || |||||||| ||| 
-agttaatttttgctttttatttttccaatg-aatatgggagcattcttgtgatgtaaatatctggtttaggtttttaattttgctaccttgataattgtagGAGTTAGTGAAAAGATATTCTGAATTCATCAACTTTCCCATATACCTCTGGGCAAGCAAAGAGGTTGATGTAGAGGTACCTGCAGATGAAGATGAGTCAA

upper sequence: AT4G24190.2 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S126_38V6.1 (Physcomitrella patens), 3'ss of exon 7
-------gaagtggttcagcattattatgaattcagtgcactgcttattcaatatttctgtttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG
        || ||    || |   || || |   |  | |||   ||      | |  | ||||   |  || | |  || ||  |||| |||       | | |||||| | |||||||  |||||||||||||| | ||||||||| | ||| ||||||||||||||||||||    || || || ||||| || |  |||    
tgacttttaattgaggaagtaactttctggaggtaagggactaaataggtggcagtgtt-tttaattttacagtctaatt-ctgttgataatt-----tgagtgcagGAACTCGTGAAGAAGTATTCTGAATTCATCAGCTTCCCTATTTACCTGTGGGCTAGCAAAGAGGTTGATGTTGAAGTGCCCGTTGAAGAGGCCGAAGAGA

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|164045346|gb|ES200905.1|ES200905
EST:     GCTGGCGAGTACCTAGAAGAAAGTAAACTTAAG                         GAATTGGTTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTG
genomic: GCTGGCGAGTACCTAGAAGAAAGTAAACTTAAGgtgggtaata ... tctactacagGAATTGG-TGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTG
EST: gi|124962446|gb|EL036869.1|EL036869
EST:     CCTAGAAGAAAGTAAACTTAAG                         GAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGG
genomic: CCTAGAAGAAAGTAAACTTAAGgtgggtaata ... tctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGG
EST: gi|163999125|gb|ES176095.1|ES176095
EST:     GCTGGCGAGTACCTAGAAGAAAGTAAACTTAAG                         GAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGG
genomic: GCTGGCGAGTACCTAGAAGAAAGTAAACTTAAGgtgggtaata ... tctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGG
EST: gi|164007678|gb|ES205456.1|ES205456
EST:     GCTGGCGAGTACCTAGAAGAAAGTAAACTTAAG                         GAATTGGTTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTG
genomic: GCTGGCGAGTACCTAGAAGAAAGTAAACTTAAGgtgggtaata ... tctactacagGAATTGG-TGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTG
EST: gi|86067432|gb|DR363189.1|DR363189
EST:     TACATCTTAGGGATGAAGCTGGCGAGTACCTAGAAGAAAGTAAACTTAAG                         GAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTC
genomic: TACATCTTAGGGATGAAGCTGGCGAGTACCTAGAAGAAAGTAAACTTAAGgtgggtaata ... tctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatttctgtttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG
                           tgctaat  putative branch site (score: 2)
      tgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagtggttcagcattattatgaattcagtgcactgcttattcaatatttctgtttatcctctcattatggttgctaatgatcattgttgtctactacagGAATTGGTGAAGAGATATTCTGAATTCATTAACTTCCCTATCTCCCTCTGGGCTAGCAAAGAGGTTGAAACCGAGGTCCCAGTTGAGGAAGATGAATCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - -ctgctta