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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG

Basic information

species Arabidopsis thaliana
transcript AT1G65430.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os08g42740.3 (Oryza sativa), 3'ss of exon 7
-gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
   |  ||||    | |    | | ||  |  || |    ||       ||||| ||   ||| |    | |||  |  |    |  ||  |   |||||||||  |||| ||||| ||||| || |||||||||||||| |||||||||||||||||||| || |||||||| || ||||| ||||| || |||||||||
gctagtccatgaatgctcaaatgtatttaaggtctttatgttgcttgaaatcat-ctaatcatgtcagatggtttatcatgttgttgatgatccttttcagGATACTGGCTAATTCTAAGCCGTGCCCAAAATGCAAACGACCAATAGAGAAAAACCAGGGATGCATGCATATGACTTGCACTCCACCTTGCAAATTTGAG

upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os09g33876.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------------------------gaaaaccattttcggtttcttctcttccatctcctagcatta-gggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
                                                                         ||| |    ||  |     | || ||     |  ||   |     || ||| | |    | | |      |||| ||   ||||    | ||      |||||| || ||  |||| ||||||||||| ||||||||||| || |||||||| || ||||| || |||||||| || ||||| || || ||||||||||||
gtttgtcgcacacataatttccttttcattcttgtatttgatagtatgtcttgtactttattctttccatcttgaatatttcttgtgtaaaatactttttttctttttaatttcctaagttcataaggaa--aaactggaagctgtttct--caagtgttgttttctcccccagGATATTAGCTTATTCTAAGCCCTGTCCGAAATGCAAACGACCTATAGAGAAGAATCAGGGATGCATGCATATGACATGCACTCCTCCTTGTAAATTTGAG

upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: LOC_Os04g41470.1 (Oryza sativa), 3'ss of exon 7
gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgc--ttcacattttgttttgttgctgctaagttccatattga-----atttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
          ||   ||| || || |     |  |||   |   ||   |  |||   | |  | |||| |      || | |  |   | |||       |||||||||| | || ||||| ||||| ||||| || ||||| ||||| || || ||||||||||| || ||||| ||||| ||||| || ||||| |||||||||
-------gactttatttttttgtcatattagtagtagttcttatgtttttactgcaagttatttcttgtgtcaactatgttgaactttctgttggttatggtttcagGATTCTAGCTAATTCAAAGCCTTGTCCTAAGTGCAAGCGGCCCATTGAAAAAAACCAGGGATGCATGCACATTACATGCACACCTCCATGCAAATTTGAG

upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM2G100913_T02 (Zea mays), 3'ss of exon 7
--------gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
        || ||   |    | |||  | |  | | |       | | |   ||||| |        ||| ||| ||  |||||      | ||| ||    ||||||||  |||| ||||| |||||||||||||| ||||||||||||||||||||||||||||| || |||||||| || |||||||| || |||||||| || 
atttaactgataattgtgaatgtttttattttattccttgtggcacttcaaattgcatgaaaaggtttattatgtatttatgctgtg----ttcatctt----ttcagGATACTGGCTAATTCTAAGCCCTGTCCAAAGTGCAAACGGCCAATAGAGAAAAACCAGGGATGCATGCATATGACATGCACCCCTCCTTGTAAATTCGAA

upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GRMZM5G876621_T01 (Zea mays), 3'ss of exon 7
gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacatttt---gttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
     ||  | ||  | |     |  ||||   |     |   |     |   |    | | | |   || |||    |||||   || ||      |||||||||  |||| ||||| ||||| ||||| |||||||||||||| || || ||||| ||||| || ||||| || || ||||| |||||||| |||||||||
---ttcctctctctctcttaatgcaaccatgcacagatctcctgtgtttttgagaaaaaaactgtccagtgttgactttgctactgtctattcatggtttcagGATACTGGCTAATTCAAAGCCTTGTCCCAAATGCAAACGGCCTATTGAAAAAAATCAGGGATGCATGCACATCACATGCACTCCACCATGCAAATTTGAG

upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv00s0207g00090.t01 (Vitis vinifera), 3'ss of exon 7
gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
  || | ||||  |     |||| |    | | |||  | || | |  ||  |  | ||  | |||   || |     | |      |  ||| ||||||||| ||||| ||||||||||| |||||||| || || |||||||| || |||||||| |||||||||||||| || ||||| || |||||||||||||||
agaatctatttgtgcaggattctttatggtttactataactatgtttaatttttttccatttgttgcaatgctaaattttatgcatgtgatgactttcagGATATTGGCTAATTCCAAGCCTTGTCCAAAGTGTAAGCGGCCAATCGAAAAAAACCAAGGTTGTATGCATATCACATGCACACCGCCATGTAAATTTGAG

upper sequence: AT1G65430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S156_28V6.1 (Physcomitrella patens), 3'ss of exon 7
gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgctt----cacattttgttttgttgctgctaagttcca-tattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
     | ||| |     |||  ||| | || |   || | |    |  |  ||  ||     | |   ||   | ||  |  | | |  |  | ||  |   ||||||| | |||||   ||| ||||| || ||||| ||| ||||||| ||||||||||| || |||||||| ||||| ||||| || || || |||||||||
----gctattctaaccctctaatct-ctatatgtaagaagtgaacttgaagatatttgtcttagagaatgacctattcttattcattatcgctgttttaaaacagGATTCTTGCAAACAGCAAACCCTGCCCCAAATGTAAAAGGCCAATTGAGAAAAACCAAGGGTGTATGCACATTACTTGCACACCTCCTTGCAAATTTGAG

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|124704071|gb|EH795473.1|EH795473
EST:     TCGGAGAATATGAATTG                         GATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAA
genomic: TCGGAGAATATGAATTGgtacgttgat ... tgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG
                                         atattgaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaaaaccattttcggtttcttctcttccatctcctagcattagggtgcatcatgcttcacattttgttttgttgctgctaagttccatattgaatttcagGATTTTGGCAAATTCCAAGCCCTGTCCAAAATGCAAACGGCCAATAGAGAAAAACCAGGGTTGTATGCATATTACGTGCACCCCACCATGTAAATTTGAG

- aaaccat
- - - - - - - - - cttctct
- - - - - - - - - - - - - -catctcc
- - - - - - - - - - - - - - - - - - - - - - - - - -atgcttc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ctgctaa