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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttttttcaatgatctaatcaaattcgagaggagatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT

Basic information

species Arabidopsis thaliana
transcript AT1G79210.3
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA08G17810.5 (Glycine max), 3'ss of exon 3
--------gttttttcaatgatctaatcaaattcga------gaggagatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT
        | || ||   |  ||||    | |  ||       | |  |  ||||        |   | |  | || |    || | |||  || |||||||| ||||||||||||||||||| || || |||||| | || |||||||||||||||||||| || 
attcattgggttcttttgtcctctagatgattgtgatcctgtaacgtaagctttagcttttgctagttcttattat-acatttgatatttgattcatgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAGCATCA

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA15G41330.1 (Glycine max), 3'ss of exon 3
------------gttttttcaatgatctaa--tcaaattcgagaggagatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT
            | || ||   |  ||||   |  |    |  | |  |  | ||        |   | |  | || |    || | |||  ||  ||||||| ||||||||||||||||||| || || |||||| | || |||||||||||||||||||| || 
tctgattcattgggttcttgtgtcttctagatttgatcctgtaatgtaagctatagcttttgctagttctaattat-agatttgatatttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTACCATCTATATTGGTTGATGAAGCATCA

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G16660.1 (Glycine max), 3'ss of exon 3
-------------gttttttcaatgatctaatc--aaattcgagaggagatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT
             |||  ||   |  |    ||    |   ||   |     | ||| | |   |||  ||| | || ||   || | |||  ||  ||||||| ||||||||||||||||||| || || |||||| | || |||||||||||||||||| | || 
tttactctctgtggttcattgggttcttgtgtcttgtagatgatttggatcctctaatgtatgctgtagttgcttat-atatttgat-tttgattcttgcagCTGCAAATGGAGTTGTCATTGCTACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA01G25940.3 (Glycine max), 3'ss of exon 3
----------gttttttcaatgatctaatcaaattcgagag--gagatttttaaggaacattgtctttggtaatcatgactgttgttttc--tttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT
           ||  ||   |  ||   ||   |    |    ||    | ||| | |  ||||  ||| |||| ||   | | |||||   ||| ||||||| ||||||||||||||||||| || || |||||| | || |||||||||||||||||| | || 
actctctgtgcttcgttgggttctcgtgtcttgtagatggtttgaatcctgtaatgtatgttgtagttg-taattatatgtttggtttttaatttttgcagCTGCAAATGGAGTTGTCATTGCCACCGAGAAGAAATTGCCATCTATATTGGTTGATGAAACATCA

upper sequence: AT1G79210.3 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv01s0011g01960.t01 (Vitis vinifera), 3'ss of exon 2
---gttttttcaatgatctaatcaaattcgaga---ggagatttttaaggaacattgtctttggtaatca--tgactgttgttttc-----tttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT
   ||    | |  | | | ||    |   | |   ||  || |||   |  |||  | |    | | ||  |||||  |  |||      ||  ||||||| | ||||| ||||| ||||||||||| |||||||| |||||||| ||||| ||||| || || 
aatgtggcataatggttttgatttgttctcaaatttggtcatatttggagttcatcttgtcccattaccaattgactaatacttttgcctgttactgcagCTGCCAATGGTGTTGTTATTGCAACTGAGAAGAAACTACCTTCTATCTTGGTGGATGAGGCATCG

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|86065878|gb|DR361635.1|DR361635
EST:     ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAG                         CTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
genomic: ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAGgttttttcaa ... ctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
EST: gi|86065881|gb|DR361638.1|DR361638
EST:     ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAG                         CTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
genomic: ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAGgttttttcaa ... ctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
EST: gi|86065890|gb|DR361647.1|DR361647
EST:     ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAG                         CTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
genomic: ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAGgttttttcaa ... ctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
EST: gi|86065889|gb|DR361646.1|DR361646
EST:     ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAG                         CTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
genomic: ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAGgttttttcaa ... ctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
EST: gi|86065879|gb|DR361636.1|DR361636
EST:     ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAG                         CTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
genomic: ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAGgttttttcaa ... ctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
EST: gi|47831532|gb|CK121216.1|CK121216
EST:     ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAG                         CTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG
genomic: ACATGCCCTAACAGCTGTTGGATCAGGCCAAACATCACTTGGAATTAAAGgttttttcaa ... ctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT
                                   ctgttgttttcttt  CT-rich tract
                                         ttttctttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttttttcaatgatctaatcaaattcgagaggagatttttaaggaacattgtctttggtaatcatgactgttgttttctttatgcagCTTCAAATGGAGTTGTCATTGCAACTGAAAAGAAACTTCCTTCTATATTGGTTGATGAAGCGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC