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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatgtggtaattgacattattttattattatcttatggtgattttacctttaattgaacttccaagatgatgagtggccacaatttctttccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG

Basic information

species Oryza sativa
transcript LOC_Os03g36790.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g36790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA17G01820.1 (Glycine max), 3'ss of exon 1
gatgtggtaattgacattattttattattatcttatggtgattttacctttaattgaacttccaagatgatgagtggccacaatttctttccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG
                                 ||     || |     || ||| |     ||      |  ||       |||  | | || | | || |||||||| | ||||||||  |  |||| ||||| | |||||||||||| |||||| |||| ||||| ||||||||  |||| |||||||
--------------------------------gtacatacatctccttctttattaactactcattcatttttgtcttttttattattctgctct-gtagATTCAATTGGTTAGAATTCAAGTTAGAGTACCTGAGTATGGTTGGACTACTCAGAAGATTTTTCATCTCATGAACTTCATTGTCAACGGAG

upper sequence: LOC_Os03g36790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: AT4G21790.1 (Arabidopsis thaliana), 3'ss of exon 1
---gatgtggtaattgacattattttattattatcttatggtgattttacctttaattgaacttccaagatgatgagtggccacaatttctttccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG
    ||    | |||||   | | |     |||| |   |||    |||  | |  |  || |||  |  |  ||  ||   | |     ||    || | |||||||| |||| || || ||  || |||||||||| | |||||||||||| |||||||| || ||||| ||||||||||| || || ||||
ttgtatagtttgattgattgtttctgtagtttatttctgggtttagttagttgtgttgcaatttctgaccttttgtttg---aaatgggattatgattggtagGTTCAACTGATAAGGATCCAAATGAGAGTGCCTGAGTATGGTTGGACTACTCAGAAGGTGTTTCATCTTATGAACTTTGTCGTCAATGGAG

upper sequence: LOC_Os03g36790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv00s2255g00010.t01 (Vitis vinifera), 3'ss of exon 1
gatgtggtaattgacattattttattattatcttatggtgattttacctttaatt----gaacttccaagatg-atgagtggccacaatttcttt------ccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG
        |||||    | ||| | |    |  | ||  || || | ||| | |     ||| |   | | ||   |  || | |  ||||| ||      |  |  | || ||||| |||| || ||| |  || ||||||| || | ||||||||| || ||||||||||||||||| ||||||||  | || || ||||
-------gaattg----tttttcactgccgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG

upper sequence: LOC_Os03g36790.1 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv10s0116g00020.t01 (Vitis vinifera), 3'ss of exon 1
gatgtggtaattgacattattttattattatcttatggtgattttacctttaatt----gaacttccaagatg-atgagtggccacaatttcttt------ccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG
        |||||    | ||| | | |  |  | ||  || || | ||| | |     ||| |   | | ||   |  || | |  ||||| ||      |  |  | || ||||| |||| || ||| |  || ||||||| || | ||||||||| || ||||||||||||||||| ||||||||  | || || ||||
-------gaattg----tttttcactgtcgtgatttgtggagttgagcttgattgttgagaaatcttatgttgtgcggttgactaagatttcattgatgtgcactgcgcagATTCAACTGATAAGGATTGAACTGAGAGTGCCAGAGTATGGTTGGACGACGCAGAAGGTTTTCCATCTTATGAACTTCATCGTCAATGGAG

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|12623091|gb|AU173304.1|AU173304
EST:     CCTTCTTCTCCCTCTCCGCCGCCTACGCGCTCGTCTCCGCCGTCGCGCTG                         GTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACC
genomic: CCTTCTTCTCCCTCTCCGCCGCCTACGCGCTCGTCTCCGCCGTCGCGCTGgtaacccccc ... ccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACC
EST: gi|38472127|gb|CF956258.1|CF956258
EST:     CCTTCTTCTCCCTCTCCGCCGCCTACGCGCTCGTCTCCGCCGTCGCGCTG                         GTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACC
genomic: CCTTCTTCTCCCTCTCCGCCGCCTACGCGCTCGTCTCCGCCGTCGCGCTGgtaacccccc ... ccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACC
EST: gi|58597378|gb|CK007906.1|CK007906
EST:     CCTTCTTCTCCCTCTCCGCCGCCGACGCGCTCGTCTCCGCCGTCGCGCTG                         GTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACC
genomic: CCTTCTTCTCCCTCTCCGCCGCCTACGCGCTCGTCTCCGCCGTCGCGCTGgtaacccccc ... ccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

acctttaattgaacttccaagatgatgagtggccacaatttctttccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG
  ctttaat  putative branch site (score: 4)
                                   caatttctttcctttt  putative PPT
                                    aatttcttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatgtggtaattgacattattttattattatcttatggtgattttacctttaattgaacttccaagatgatgagtggccacaatttctttccttttgaagGTTCAATTGATCAGAATTCAGTTGCGAGTGCCTGAATTTGGTTGGACTACCCAGAAGGTTTTCCATCTGATGAACTTTGTTGTAAACGGAG

- - - - - - - - - - - - - - - tcttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - atgatga