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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactctttcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA

Basic information

species Oryza sativa
transcript LOC_Os01g57220.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G169773_T02 (Zea mays), 3'ss of exon 4
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactcttt---cttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA
  ||| |   ||||||||  ||||||  ||     || |||| ||  ||| ||  ||  ||   |  ||      |   || ||||   ||||  |||  ||||||| |||||||||||||| || || |||||||||||  | || |||||||||||||||||||| || ||||||||||| ||||| ||||||||||| ||
-actaattaagctaatttgttgctta--ttgcccatgctgcagtccttttacctgttaggtctgtcttttaataataataccctttttcctttcgtttggcagCTGGTATTGTCATTGAAGATAAGAATTGGCCACCCTTTATGCCCATTATTCATCATGACATTTCGAACGAGATACCAATTCACCTGCAAAGGATGCAGTA

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA06G45160.1 (Glycine max), 3'ss of exon 5
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactctttcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA
   ||||   | | || |  |  ||||      ||   |  | |    | |  ||||| |||     |  |  || |  | | ||| ||||  ||| ||||||| || || || || |||||||| |||||||| || ||||| || ||||||||||||||| |||| || |||||| | || || |||||||| || ||
--gtatttgagttcatctattctttataga-aatcaactagagtgatgtctgtattttggtt-----tcttaactctttatttttttttttcatttgcagCTGGAATAGTTATAGAGGAGAAAAATTGGCCACCTTTTTTCCCCATCATTCATCATGACATTGCAAAGGAAATACCAGTACATCTTCAAAGGATCCAGTA

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT2G20840.1 (Arabidopsis thaliana), 3'ss of exon 4
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactctttcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA
   |||  |||  ||| || | ||| |||     |   ||  || |   |||||| | |  || |  | ||| |       ||||| ||||  |    ||| || ||||| || |||||||||||||||||||| || || ||| | || |||||||||||||||||||||||||| ||||| || || || || |||||
--gtatctttgtcaatattat-cttttgtagaaac--ctgacattt-cgttccatgtgaaatgctcatgctgtca------tctttattttggt----agCCGGAATTGTGATAGAAGAGAAAAACTGGCCACCGTTTTTTCCTCTCATCCATCATGACATTTCAAATGAGATACCCATCCATCTGCAGAGAATCCAATA

upper sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv12s0059g01930.t01 (Vitis vinifera), 3'ss of exon 4
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttc-cattttagttgttgcttctgcctttcaactctt-tcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA
          | |  | |  || |||| |   |  ||   ||||    ||    | | |  |  |    ||| |  |  || | |  |  ||| |||  ||||||| |||||||| || |||||||| |||||||| || |||||  ||||||||||||||||| ||||||| ||||||||||| | ||| | | |||| ||
----------gtttgtctgttgtttatatcattagtgaatcaattaggttgagtagtgttttcatgcagtctacaatctaaatatcattctttctttggcagCTGGAATTGTCATAGAGGAGAAAAATTGGCCACCATTTTTCCCCCTTATTCATCATGACATTGCAAATGAAATACCAATCCATCAACAGAAGTTGCAGTA

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|11370676|gb|AU164981.1|AU164981
EST:     GAATTGAGAAGAAGAGAAGAAGCTGCATCCAGAG                         CTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTC
genomic: GAATTGAGAAGAAGAGAAGAAGCTGCATCCAGAGgtatattttt ... tatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTC
EST: gi|286756|gb|D15563.1|D15563
EST:     GAATTGAGAAGAAGAGAAGAAGCTGCATCCAGAG                         CTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTNTTCCCTA
genomic: GAATTGAGAAGAAGAGAAGAAGCTGCATCCAGAGgtatattttt ... tatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattttccattttagttgttgcttctgcctttcaactctttcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA
                  ttgcttctgcctttca  CT-rich tract
                                    tctttcttttattttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggctattcttgctaattttgtgcttatgtttgttctgttgcaatctattttccattttagttgttgcttctgcctttcaactctttcttttatttttcagCTGGGATTGTCATTGAAGAGAAAAACTGGCCACCCTTCTTCCCTATTATTCATCATGACATTTCAAATGAGATACCAATCCACCTACAAAGGATGCAATA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG