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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatgctcaaaaatgaattggttctcacaaaagttcatcatctttccggaccatcagtaataaacctgttcaaattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC

Basic information

species Arabidopsis thaliana
transcript AT2G34560.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: LOC_Os01g55260.1 (Oryza sativa), 3'ss of exon 8
-----------------------------------------------------------------------gtaaaat----gctcaaaaatgaattggttctca-caaa-agttcatcatctttccggaccatcagtaataaacctgttcaaattt--tgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
                                                                        |||  |    |||  ||| ||       || || |||| | | | |||  ||||         |    ||   ||||  |  |||  ||||||||||||| ||    || ||||| ||  | ||||||||  | |||||||||||| | || |||||||| || |||||||||||||| || || |||||||
gtttctgcttgtttgaacatatcaaaattaagcttgctagtgtagcactccaagtcacggtttcctacttcataatctttcagcttgaaactgtcccaactcccaacaaacaatacgtcagatttcaaagtttcta----tatttctgtcaatgtttactgcagATGGATGGCTTGACAAAGACGAACGACTTGGTATTTGTACTTGCAGCAACAAATTTACCTTGGGAACTGGACGCAGCTATGCTCCGCCGGCTTGAGAAAC

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G115766_T02 (Zea mays), 3'ss of exon 7
------gtaaaatgctcaaaaatgaattggttctca---caaaagttcatcatctttccgg-----accatca-gtaataaacctgttcaaattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
      ||      ||  | ||  || ||||  |||        |    |  ||| |  ||     |  ||    | | |      ||  | |  ||||||||||||||||    || ||  ||||||| || |||||| |||||||||||||| | || |||||| | |||||||| ||||| || || || ||||| |
ccacaagtgtccctctggacaaccaactggtcttcagttttggggactgttgtctctatggtattgattatttcatgacattttgattttattgctgcagATGGATGGGTTGACTAAGACAGATGAGCTTGTTTTTGTTCTAGCAGCAACAAATTTACCATGGGAATTGGATGCAGCAATGCTGCGTCGGCTGGAGAAGC

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 8
--gtaaaatg-ctcaaaaatgaattggttct--cacaaaagtt--catcatctttccggacca-----tcagtaataaacctgttcaaatt----ttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
   | |  |   | |  | | | |||  | |  ||  | ||||  |||     ||| ||         |||  ||| || |  ||   |||    |||||||||||||| ||    || ||  |||| || || ||||||||||| ||||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| |
ccatgacttaatttattagttatttgagtttaccatgatagttggcatatgtattctggtgtgctttctcaaaaattaatc-atttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTAGCGGCAACAAATCTTCCCTGGGAACTGGATGCAGCCATGCTTCGACGTCTTGAGAAGC

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GLYMA05G26100.2 (Glycine max), 3'ss of exon 3
---gtaaaatgctcaaaaatgaattggttctcacaaaag--------ttcatcatct-ttccggaccatcagtaataaacctgttcaaatt----ttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
    | |||  ||  |   | |  || ||||||  || |        |   || |||  |  |     |||  ||| || |  ||   |||    |||||||||||||| ||    || ||  |||| || || |||||||| || ||||||||||| ||||||||| | |||||||| |||||||| ||||| ||||| |
aaattcaaactctgcatcttaatatgcttctcatcaatggagtgacatatgtcttctgctgtgctttctcaaaaattaatc-atttggattaagattgcagATGGATGGTTTGACAAAGACAGATGAACTGGTTTTTGTTTTGGCGGCAACAAATCTTCCCTGGGAATTGGATGCAGCCATGCTCCGACGTCTTGAGAAGC

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 8
-----------------------gtaaaatgctcaaaaatgaattggttctcacaaaagttcatcatctttccggaccatcagtaataaacctgttcaaattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
                        |  | |  |   | ||||||    | ||||   |  | ||  | | || | |     | | || |    | | | ||  ||||||||||||| ||    || ||  ||||||| || |||||||||||||||||||||||||| |||||| | |||||||| |||||||| || || || ||  
acagataactaactctgaatattttttattcattggagatgaatcaaatatcacttcaact-atactttctcagaa-----attgatgacttggattagat--tgcagATGGATGGTTTGACAAAGACAGATGAGCTTGTTTTTGTTTTAGCAGCAACAAATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGA

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ09429 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaatgctcaaaaatgaattggttctcacaaaagttcatcatctttccggaccatcagtaataaacctgttcaaattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
                                   |||          |   |   |   | |  ||| || |    |||   |||||||||| ||   | || | || || || || || || || ||||| |||||  |||| ||||||||||| || || |||||||||||||| |||||||
-----------------------------------gttgggaggaaagctccagtgtagctgacgaacttggt----tttgttagATGGATGGCTTGATGCAAGCCAACGATCTGGTGTTCGTCTTGGCAGCCACAAACATCCCATGGGAACTAGACGCGGCAATGCTCCGGCGTCTCGAGAAAC

upper sequence: AT2G34560.2 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: EFJ34591 (Selaginella moellendorffii), 3'ss of exon 4
gtaaaatgctcaaaaatgaattggttctcacaaaagttcatcatctttccggaccatcagtaataaacctgttcaaattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
                       |||   |  |||| ||           | |   |   | |  ||| || |    |||   |||||||||| ||   | || | || || || || || || || ||||| |||||  |||| ||||||||||| || || |||||||||||||| |||||||
-----------------------gttgggaggaaagctc-------cagtgtagtgtagctgacgaacttggt----tttgttagATGGATGGCTTGATGCAAGCCAACGATCTGGTGTTCGTCTTGGCAGCCACAAACATCCCATGGGAACTAGACGCGGCCATGCTCCGGCGTCTCGAGAAAC

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|47831791|gb|CK121475.1|CK121475
EST:     GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAG                         ATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACA
genomic: GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAGgtaaaatgct ... aattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACA
EST: gi|125070584|gb|EL135940.1|EL135940
EST:     GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAG                         ATGGATGGGTTACAGAAA
genomic: GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAGgtaaaatgct ... aattttgcagATGGATGGGTTACAGAAA
EST: gi|124765937|gb|EH856067.1|EH856067
EST:     GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAG                         ATGGATGGGTTACA
genomic: GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAGgtaaaatgct ... aattttgcagATGGATGGGTTACA
EST: gi|124961297|gb|EL035840.1|EL035840
EST:     GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAG                         ATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTT
genomic: GCAGTGAACATGAAGCTAGCAGGCGTCTCAAAACCGAGCTGCTCATTCAGgtaaaatgct ... aattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

caaaagttcatcatctttccggaccatcagtaataaacctgttcaaattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC
                                         ttcaaatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaaatgctcaaaaatgaattggttctcacaaaagttcatcatctttccggaccatcagtaataaacctgttcaaattttgcagATGGATGGGTTACAGAAAACGAATGAGCTCGTATTTGTTTTAGCAGCAACAAATCTCCCCTGGGAACTAGATGCAGCTATGCTCCGGCGTCTAGAGAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT