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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgattattttttatatgttcttgctaaagatttatgagtcttttcttatgtgatgttttgatgctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA

Basic information

species Arabidopsis thaliana
transcript AT5G28840.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: LOC_Os10g28200.1 (Oryza sativa), 3'ss of exon 3
----gtttgtgattatt-ttttatatgttcttgctaaagatttatgagtct-----tttcttatgtgatgttttgatgctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
    ||   | |  ||  |||||    ||  || ||    ||  | |  |      ||  ||   |  |||||| |      |  ||||||||||||| |||||||||||||||||||| || |||||| | || ||||| |||| ||| || ||||| |||||||| ||  ||||  | ||||| |
gtttgtccatcaaaataattttaggctttagtgttatgttttagtaaaaccagaagttgatttcctactgttttaactactgtccagCCTCAAGATGCCTATGGTTTGGAGAAGCTTGCAACTGAGGAGCTCTGCAAGCACTACACCAAGGACTTTGGCATTGAGTGCCGTGTTGGCCGCTTCCACA

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G124434_T01 (Zea mays), 3'ss of exon 3
----gtttgtgattattttttatatgttcttgctaa--agatttatgagtcttttcttatgtgatgttttgatgct--gatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
    |||  |    ||    |  | |||| || |    |||  |||      |    | |        | | || |  | |  ||||||||||||| ||||| |||||||||||||| || |||||| |||| ||||| |||| ||| || ||||| || ||||| ||  | ||  | ||||| |
gtgtgttcatcgaaatacaatg-acgttcctgtttgttagacatatatacagtcaaatctaaatcccctcggtgttacgtttcagCCTCAAGATGCCTATGGCTTGGAGAAGCTTGCAACCGAGGAGCTGTGCAAGCACTACACCAAGGACTTTGGCATCGAGTGCCGCGTCGGCCGCTTCCACA

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G43400.1 (Glycine max), 3'ss of exon 3
-------------gtttgtgattatttttt--atatgttcttgctaaagatttatgagt-cttttctta--tgtgatgt-tttgatgctga------tatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
               || | |||| || ||  |  | |||| | ||   | ||   | | |||   |||   | ||| | ||| ||  |        ||||||| |||||||| |||||  ||||||||||||| || || ||||| || |||||||| ||||| |||||||| |||||||| || ||||| || |||||||
gtttgttgctgattcttttaattagttgttcaacttattctggttattcacttgaaaatacttaggttagcagggatatatttaatatttgactttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGGATTGGGAGATTCCATA

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA03G40720.1 (Glycine max), 3'ss of exon 3
-------------gtttgtgattattttttata--tgttcttgctaaagatttatgagtcttt--tcttatgtg---atgttttgatgctga----tatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
               ||   |||| || ||  |  | |||| | ||   | |||  | |  ||   ||     |   || |||   |  |||    ||||||| |||||||| |||||  ||||||||||||| || || ||||| || |||||||| ||||| |||||||| |||||||| || ||||| || |||||||
gtatgttgctgattctttgaattacttgttcaagttattctggttattcacttaaaaatacttaggctagcagggatatatttaatttttgacttttatagCCACAAGATGCATATGGGCTGGAGAAGCTTGCAACAGAAGAGTTATGCAAGCATTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGATTCCATA

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA20G36740.2 (Glycine max), 3'ss of exon 3
-------------gtttgtgattattttttatatgttcttgctaaagattta---tgagtctt---ttcttatgtgatgttttgatgctgatat-agCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
              |||   ||| ||   | ||||||  | ||  |  || |   || |  |    ||  | |||    |||||   ||| | | |||| |||||||| |||||  | ||||||||||| || ||||| || || ||||| || ||||| |||||||| |||||||| || ||||| |||||||| |
gtttgttggtgatcttttcaattgttcaatttatgttggttcttgattttcacattgggattgggattaatgtgtttaattttgtgactgtttttagCCACAAGATGCATATGGGCTAGAGAAGCTTGCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACA

upper sequence: AT5G28840.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G30400.1 (Glycine max), 3'ss of exon 2
-------------gtttgtgattattt--tttatat--gttcttg--ctaaagatt--tatgagtcttttcttatgtgatgttttgatgctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
              |||   ||| ||   ||||| |  |||||||   |  | |||   ||  |  ||   || | | || || |||   |  | |||||||||||||| |||||  | ||||| ||||| || ||||| || || ||||| || ||||| |||||||| |||||||| || ||||| |||||||| |
gttagttggtgatcttttgaattgttcaatttatgttggttcttgattttcacattgggattgggattaatttgtttaattttgtgactttttt-tagCCTCAAGATGCATATGGGCTAGAGAAACTTGCAACAGAGGAATTATGCAAGCACTATAACAAGGATTTTGGAATTGAGTGCCGCATTGGGAGGTTCCACA

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|116412576|gb|EG455168.1|EG455168
EST:     TCAGATGCTTGTCCTGCAGAG                         CCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAG
genomic: TCAGATGCTTGGCCTGCAGAGgtttgtgatt ... gctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAG
EST: gi|164177977|gb|ES109683.1|ES109683
EST:     TGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG                         CCTCAAGATGCTTATGGTTT
genomic: TGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGgtttgtgatt ... gctgatatagCCTCAAGATGCTTATGGTTT
EST: gi|86019686|gb|DR315432.1|DR315432
EST:     TGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG                         CCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAG
genomic: TGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGgtttgtgatt ... gctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAG
EST: gi|116460304|gb|EG502896.1|EG502896
EST:     TGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAG                         CCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAG
genomic: TGGAGACTACTAATGTGAGCTTGAAGGAGTCAGATGCTTGGCCTGCAGAGgtttgtgatt ... gctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcttgctaaagatttatgagtcttttcttatgtgatgttttgatgctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA
       taaagatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgattattttttatatgttcttgctaaagatttatgagtcttttcttatgtgatgttttgatgctgatatagCCTCAAGATGCTTATGGTTTGGAGAAGCTTGCTACGGAGGAGTTGTGTAAGCATTACAACAAAGATTTTGGTATTGAGTGTCGAATTGGAAGGTTCCATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG