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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tctttatggcttttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG

Basic information

species Oryza sativa
transcript LOC_Os01g62420.4
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G146206_T02 (Zea mays), 3'ss of exon 5
--tctttatggct--tttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtctttt-ttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
  |  |    |||  ||||   |  |||       || || ||    | ||||| | ||      | |||| |   ||| |  |    ||| |  | |||| |||| || ||||| |||||||| ||| |||| ||||||||||||||||||||||| ||||| |||||||| |||||||| ||||||||||||||||||
cattctagctgctgctttgaattttattccttcacgcagaaatgagggacttctgaatt-----tctctaattcactgtttactgcctctccttttgttttgcagAAAAAATATCAGATTGGACAAATATTGTGTTGGCATATGAACCAGTTTGGGCTATTGGTACCGGCAAAGTTGCAACTCCTGCTCAGGCTCAGGAG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA13G41120.1 (Glycine max), 3'ss of exon 5
--tctttatggcttttgtggtccattgtactgtgctgacatagaagt-cttctcatttctccacc--cctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
  |    |   || || |  |   ||  || |   |  |||   |   |||   ||||    | |   |||  |||| |      |||   ||     ||| |||  || |||||  |||||  |||||| |||||||| ||||| |||||||||||||||||||| || ||||||||||| |||||||||||||| |||
gttaaaaaaaactgttctaattgctttaacag-attatcatctcatcacttgctattttgttagcaatctatattttcgctgaccttaagtgta----tttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTATGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCAACTCCTGCTCAGGCTCAAGAG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G04290.2 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------tctttatggcttttgt-----ggtccattgtactgtgctgacatagaag--tcttctcatttctccacccctaacttttt-----gtct---tttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG-----
                                                                             |||||   | | ||||          |   | |     ||   ||  ||  | |  | || ||  |||     | ||| |      |||   ||||  ||   | || || |     |||  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| |||     
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAGGTATG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA15G04290.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------tctttatggcttttgt-----ggtccattgtactgtgctgacatagaag--tcttctcatttctccacccctaacttttt-----gtct---tttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
                                                                             |||||   | | ||||          |   | |     ||   ||  ||  | |  | || ||  |||     | ||| |      |||   ||||  ||   | || || |     |||  || |||||  |||||  |||||| |||||||| || || |||||||||||||||||||| || |||||||| || |||||||||||||| |||
gtaccttttttctccgtatatacaggtttaattttctgcgtattcattaagtcgtgtttttatctcagatttggaggtctttgctgttcttgtttaaaaaaaaaaaattcctaattgctttaacagattatcattatctcatcacttgctattttgttagcaatctatattttcgctgaccttaattgtatttgcagCTAAAATATCAAATTGGGACAATGTCGTTTTGGCCTACGAGCCAGTTTGGGCCATTGGAACAGGAAAGGTTGCTACTCCTGCTCAGGCTCAAGAG

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G55440.1 (Arabidopsis thaliana), 3'ss of exon 5
---------------------------------------------------------------------tctttatggcttttgtggtccatt----gtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatattttt-----cagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
                                                                     | || |||    |  ||  |  ||    | ||| | ||  | |||        |||   | |        | || ||| ||     |||| |  | ||  |     ||||   | |  |  | ||| | ||||||||  | || ||||||||||| ||||||||||||||||| ||||| || | ||| || || ||||| || 
gtatgtatattgtcaaacatttaatctctttttgctatctcagttcgttctcgtttacagtgagacctgttttgatgatagtgatgcccgtttctacgcactatactcccttagtgtgtgattcaaaccccacagaaatatttgttggctaaaaaactctttttgttggtaatggcagATCGGGTGACAAACTGGTCAAATGTTGTCATAGCCTATGAACCAGTGTGGGCCATTGGAACCGGAAAGGTCGCTAGCCCAGCCCAAGCTCAAGAA

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv06s0004g04800.t01 (Vitis vinifera), 3'ss of exon 5
tctttatggcttttgtggtccattgtactgtgctgacatagaagtct-tctcatttctccacccctaactttt-tgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
 ||  |||  |||     |      ||      |    |||  || | | |  | | |  ||   ||  |||  ||  |  ||| ||  |  | | ||||||| ||  | ||    |||   ||| |||||||||| |||||||| |||||||||||||| || || ||||||||||||||||||||||| ||||| 
-ctacatgaatttgtaattgtgccatatcccttttttctagctgtatgtgttctctatgaacggatatgtttgatgaataatttgct-attttctctttcagAAAAAGTGTCAAGCTGGGATAATATTGTTTTGGCTTATGAACCTGTTTGGGCCATTGGCACTGGAAAGGTTGCAACCCCTGCTCAGGCACAGGAA

upper sequence: LOC_Os01g62420.5 (Oryza sativa), 3'ss of exon 4
lower sequence: EFJ31929 (Selaginella moellendorffii), 3'ss of exon 5
tctttatggcttttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG-----
                               | |    |   | | || | || | | || ||  | ||     ||     ||||  |    | |  |||| ||| |    || ||||  ||||| ||  | ||||| || ||||| ||||| |||||||| || || ||||| |||||||| ||||||||||||     
-------------------------------gtttgggtttca-tgtttttatct-tgcatccaaagctcacactcaagcatacttcttgattgtggcagACAAGGTCAAGGACTGGAAGAATGTGGTGATAGCATACGAGCCAGTGTGGGCGATTGGAACAGGAAAAGTTGCCACCCCTGCGCAGGCTCAGGAGGTCCA

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|27576926|gb|CA999620.1|CA999620
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|58597190|gb|CK007718.1|CK007718
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTAGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|163928335|gb|EG712603.1|EG712603
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGC--ATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33691551|gb|CF319790.1|CF319790
EST:     GCAGGAACAACGATGTGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: GCAGGAACAACGATG-GAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33693382|gb|CF321621.1|CF321621
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATACGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|27576424|gb|CA999118.1|CA999118
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
EST: gi|33690114|gb|CF318353.1|CF318353
EST:     AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAG                         AGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG
genomic: AGCAGGAACAACGATGGAAGTTGTTGCAGCGCAAACTAAAGCTATTGCAGgtaatttcac ... tatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG
                ccctaac  putative branch site (score: 2)
                                             tatttttc  putative PPT
                       tttttgtctttttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tctttatggcttttgtggtccattgtactgtgctgacatagaagtcttctcatttctccacccctaactttttgtcttttttactcgtcatatttttcagAGAAGATATCCGATTGGACCAATGTTGTTTTGGCATATGAACCAGTTTGGGCCATTGGAACCGGCAAGGTTGCAACCCCTGCTCAGGCTCAGGAG

- - - - -cttttgt
- - - - - - - - - - - -tgtactg
- - - - - - - - - - - - - - - tgctgac