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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttactcatatgcttaatctcaatagaacctcaaaaacacattcctttttttgaattagcatggtttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG

Basic information

species Arabidopsis thaliana
transcript AT3G28900.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g33920.1 (Oryza sativa), 3'ss of exon 2
ttactcatatgcttaatctcaatagaacctcaaaaacacattcctttttttgaattagcatggtttcttaagctttactttctatg------tttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
      |||   ||    ||   | |    | | |  || || || | |   | ||  | ||| |  ||   ||| |   | |||       | | |||||| |||||||| || ||||| |||||||||||||| ||||| |||||| | ||||||   ||||| ||||| ||| |||||||||| || || ||||||  ||| |
-----gataccgtttggttcttcatattaccgatattacttttctctatgctatttcac-tggatatttgtacttgaggatttatacagtgttctattttctccagATTCCCCACTTGAGGCCTGCTGAGTACAAGAGGTCCAGGTTGTCTAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGAGTGCTCTCTGGAACTGCAG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: LOC_Os08g06040.1 (Oryza sativa), 3'ss of exon 2
--ttactc---atatgcttaatctcaatagaacctcaaaaacacattcctttttttgaattagcatggtttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
  ||  |    ||| | ||  | | ||  |       ||    ||||  |    ||| | || | | | ||||||  |     |   | || |      ||||||||||| ||  ||||||||||||||||||| ||||| || ||| |||||||    ||||| ||||| ||| | || |||||||| || |||||   ||| |
aattggttgaaataagttttctttgaaccggtatcttaagcttcattgttaacattgcaatatccttggttctta--caaagttgcttgtgctaaa---ctgcagATTCCACACCTGAGACCTGCTGAGTACAAGAGGTCCAGATTGTCAAGGAATCGCAGGACCGTGAACCGTCCTTACGGTGGTGTCCTGTCTGGTACTGCAG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G152573_T04 (Zea mays), 3'ss of exon 2
ttactcatatgct-taatctcaatagaacctcaaaaacacattcctttttttgaattagcatggtttcttaagctttact--ttctatgtttgttt--tctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
    ||| ||  |  | ||| ||    ||  |   |  | |    | |      |  |||||| ||   | |   | |    |     |  || ||    |||||||||| ||  ||||||||||||||||||| ||||| ||||||||||||||| | ||||| ||||||||| |||||||||||||||| |||||   ||| |
----tcagattatgcagtcttaagttcacg-cgggagtataagtttgtgccattaacagcatgtttaactgattctcataaatatcgcgaatgcttgaattgcagATTCCACACCTGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCAAAGGACTGTGAATCGTCCATATGGTGGTGTTCTGTCTGGTACTGCAG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G032564_T01 (Zea mays), 3'ss of exon 2
-----ttactcatatgcttaatctcaatagaacctcaaaaacacattcctttttttgaattagcatggt-ttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
     |||  ||  |  | | | |  |  | |    ||       |   ||   |   |||    || |  || |||    || || ||||| ||   ||  ||||||||| ||  ||||||||||||||||||| ||||| |||||||||||||||   ||||| ||||| ||| |||||||||||||||| |||||    || |
tcagattaggca-gtcttaagtttgcactgcagtataagtttgtgtcatttacataatatttaactgctgctcataaa---tatttcctatgcttcaatt--gcagATTCCACACCTGAGACCTGCTGAGTACAAGAGGTCCAGGTTGGCAAGGAACCGCAGGACTGTGAACCGTCCATATGGTGGTGTTCTGTCTGGTACCGCAG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G152552_T01 (Zea mays), 3'ss of exon 2
ttactcatatgcttaatctcaatagaacctcaaaaacacattccttt-ttttgaattagcatggtttcttaagctttactttctatgtttgt-tttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
 |||    |   |    |||| |   |||  ||      |||| | | |  |    ||        |  ||   |||| |     |||||   | | | ||||| || || ||||| |||||||||||||||||||| |||||| | |||| |   ||||| ||||| ||| | |||||||| || || |||||| ||||||
-tacctgaacaat-gccctcagtgtcaccaaaactgggtattcatctgtcattggatatttccacctaatattgtttaatgctattgtttccatatttccagATCCCTCACTTGAGGCCTGCTGAGTACAAAAGGTCCAGGTTGCCTAGGAGCCGCAGGACTGTGAACCGTCCTTATGGTGGAGTACTCTCTGGAATTGCTG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G166963_T01 (Zea mays), 3'ss of exon 2
--ttactcatatgcttaatctcaatagaacctcaaaaacacattcctttttttgaa--ttagcatggtttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
    |  ||| | | |  |||  |     ||| |  |  || |  || | || | |  | | | ||||| || |  |     |   |   ||  |||| | |||||||| ||| |||| || ||||||||||||||||| |||||| | ||||||   || || ||||| ||| | ||||| || || |||||||||  ||| |
gaggatgcatgttcatgttctacaatttgccttattattacttgtctgtgttggcagttcatcttggttgctcacaccgagatggtt---ttcatttttt-cagATTCCCCATCTGAGGCCAGCTGAGTACAAAAGGTCCAGGTTGTCTAGGAACCGCAGAACTGTGAACCGTCCCTATGGGGGAGTACTATCTGGAACTGCAG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GLYMA09G37360.1 (Glycine max), 3'ss of exon 2
ttactcatatgcttaatctcaatagaacctcaaaaacacattcctttttttgaattagcatggt-ttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
||| | |  |  || |||  |||| | ||  ||  |   ||     ||    |||  || | || || | | | |||  |     ||  | |  |||||||||||| || |||||||||||||| ||||| ||||| || ||| |  |||||   ||||| || || || || || || |||||| |||| ||||  ||||
ttaattaagttgtttatccaaatacatccctaagtagtgatgagcattgagcaatatgccttgtattatcatgattttttgatcctgact-taatctgcagATTCCACACTTGAGACCTGCTGAATACAAGAGGTCTAGATTGCCTCGGAACCGCAGGACCGTAAACCGAGCCTACGGAGGTGTTTTATCAGGAGGAGCTG

upper sequence: AT3G28900.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv14s0108g00850.t01 (Vitis vinifera), 3'ss of exon 2
ttactcatatgcttaatctcaatagaacc----tcaaaaacacattcctttttttgaattagcatggtttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
 |   || |   || |  |   |  |       | | || || ||   | |  || ||||       ||| ||    |  | ||  |   | |    |||||||||||| ||  ||||||||||||| ||||| ||||| || ||| ||||||||   ||||| ||||| || || ||||| |||||| | || || | |||||
gtggccagagttttcacttgtgtttacttgtgattagaaccatatat-tctgcttcaattgtgtcaattttttcttttacaattctttgatcta---tctgcagATTCCTCACCTGAGACCTGCTGAATACAAGAGGTCTAGATTGCCAAGGAACCGTAGGACTGTGAACCGGGCCTATGGAGGTGTTTTGTCGGGTGGTGCTG

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|86081909|gb|DR377668.1|DR377668
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|124836143|gb|EH920582.1|EH920582
EST:     TACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: TACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|152038453|gb|AV823465.2|AV823465
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027917|gb|DR323670.1|DR323670
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027914|gb|DR323667.1|DR323667
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027921|gb|DR323674.1|DR323674
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027920|gb|DR323673.1|DR323673
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027912|gb|DR323665.1|DR323665
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027922|gb|DR323675.1|DR323675
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027915|gb|DR323668.1|DR323668
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027924|gb|DR323677.1|DR323677
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTAYVAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027918|gb|DR323671.1|DR323671
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|86027919|gb|DR323672.1|DR323672
EST:     AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: AGAGAGCTAGTGGACCTAAGTGCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
EST: gi|164011925|gb|ES065660.1|ES065660
EST:     GCCCTGTTACTGGCAAGAGAATCCAAGGG                         ATTCCACATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC
genomic: GCCCTGTTACTGGCAAGAGAATCCAAGGGgtaatctttt ... ttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttttgaattagcatggtttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG
                                         tttgttttct  CT-rich tract
                  tttcttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttactcatatgcttaatctcaatagaacctcaaaaacacattcctttttttgaattagcatggtttcttaagctttactttctatgtttgttttctgcagATTCCGCATTTGAGACCTGCTGAGTACAAAAGGTCAAGGTTGGCAAGGAACGAGAGGACAGTGAATCGTGCATATGGTGGTGTTCTATCTGGAGTTGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- actcata
- - - - - - - -atctcaa
- - - - - - - - - - - - - - - caaaaac