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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aactcaaagtagtttttttttggtgattgtgttttgattttagcaaagagtggattttttcttgatgtgttgagattgatgaattgtatttgaaatgcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAGGTGAACGGTAACGA

Basic information

species Arabidopsis thaliana
transcript AT2G23930.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G23930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: GRMZM2G083642_T02 (Zea mays), 3'ss of exon 2
aactcaaagtagtttttttttggtgattgtgttttgattttagcaaagagtggattttttcttgatgtgttgag-attgatgaattgtatttgaaat---gcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAGGTGAACGGTAACGA
   |   | |  ||||||| |  ||    || |   |||  |  ||    | |   ||    | ||  || |   ||   ||  |||| | |  | |    |||| ||| | ||||| |||||  | ||||  || || ||||||||||| || |||||||||||||| || ||||| |||||||| ||||| || || || ||
---ttttatttatttttttatcttggagatgctac-attagattaatattttgccattgaaattataagtggcttatgtgtgcgttgtttgtccatttcttcagTTAAGATGAATGCAAACCGTGTTGTTATCGGCACACTTCGTGGGTTCGACCAGTTCATGAATCTGGTGGTGGACAACACTGTGGAGGTCAATGGAAATGA

upper sequence: AT2G23930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: Vv08s0007g03130.t01 (Vitis vinifera), 3'ss of exon 2
aactcaaagtagtttttttttggtg-attgtgttttgatt-ttagcaaagagtggatttttt----cttgatgtgttgagattgatgaattgt-atttgaaatgcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAGGTGAACGGTAACGA
      |||    || |   || || |||  || ||  ||  |||  |  | |  || |       ||| |     ||| ||| |  | | || ||||  | |||||||||| | ||||| ||||| |||||   ||||||||||||||||||||| ||||||||||| || || ||||| |||||||| || ||||| || || ||
------aagccccttgtgcatgatgcattaagtattagttgctagagactaatatatctgaaaaaacttcagaacgtgaaattta-aactggtgatttatattgcagTCAAGTTGAATGCAAACCGGATGGTGGTTGGAACTCTTCGTGGGTTTGACCAGTTCATGAACCTGGTGGTGGACAACACTGTGGAAGTGAATGGAAATGA

upper sequence: AT2G23930.1 (Arabidopsis thaliana), 3'ss of exon 2
lower sequence: PP1S475_6V6.3 (Physcomitrella patens), 3'ss of exon 1
------aactcaaagtagtttttttttggtgattgtgttttgattttagcaaagagtggattttttcttgatgtgttgagattgatgaattgtatttgaaatgcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAGGTGAACGGTAACGA
         | ||  |||| |   ||  |  |      | ||| |  | |  ||  | |  || |  |||   || | | |    |   | || ||||     |||||||||| ||||||    | |  |||  ||||   || ||||| ||||| ||||||||||| |||||  ||||||||||||||||| | || |||   ||
aaacgagtgttaagttagtgtccattgagccagaaaaatctgaatccaacttagt-tagtattctaattggcttgatcaaacgcttcggtggtctttg-----cagTCAAGCTCAATGCTGGTAGGAATGTTGTTGGAGTCCTGCGTGGATTTGACCAGTTCATGAACCTTGTACTGGATAACACTGTTGAGATCAATGGTGCTGA

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|125281568|gb|EL295653.1|EL295653
EST:     CTTAAGAAGTACATGGATAAGAAGCTCCAAA                         TCAAGCTTAATGCTAACCGAATTGGTTACTGGAACTCTTCGTGGGTTTGAT
genomic: CTTAAGAAGTACATGGATAAGAAGCTCCAAAgtaagttcaa ... tgaaatgcagTCAAGCTTAATGCTAACCGAA-TGGTTACTGGAACTCTTCGTGGGTTTGAT
EST: gi|124756277|gb|EH846407.1|EH846407
EST:     TAAGAAGCTCCAAA                         TCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATC
genomic: TAAGAAGCTCCAAAgtaagttcaa ... tgaaatgcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATC
EST: gi|164107895|gb|ES111649.1|ES111649
EST:     AAGTACATGGATAAGAAGCTCCAAA                         TCAAGCTTAATGCTAACCGAATG
genomic: AAGTACATGGATAAGAAGCTCCAAAgtaagttcaa ... tgaaatgcagTCAAGCTTAATGCTAACCGAATG
EST: gi|47830339|gb|CK120023.1|CK120023
EST:     AAGTACATGGATAAGAAGCTCCAAA                         TCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATC
genomic: AAGTACATGGATAAGAAGCTCCAAAgtaagttcaa ... tgaaatgcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aagagtggattttttcttgatgtgttgagattgatgaattgtatttgaaatgcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAGGTGAACGGTAACGA
                            gattgat  putative branch site (score: 4)
                                    aattgtatttgaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aactcaaagtagtttttttttggtgattgtgttttgattttagcaaagagtggattttttcttgatgtgttgagattgatgaattgtatttgaaatgcagTCAAGCTTAATGCTAACCGAATGGTTACTGGAACTCTTCGTGGGTTTGATCAGTTCATGAATCTTGTTGTGGATAACACTGTTGAGGTGAACGGTAACGA

-actcaaa
- - - - - - - - tttttgg
- - - - - - - - - - - - - - -tgttttg
- - - - - - - - - - - - - - - - - - - - - -caaagag