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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgttattgctagcatgttcttattatatcaaatagttttccgcttgtagatttttgttatgttaataagtactgacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGAAGAGAAAGACGCTC

Basic information

species Oryza sativa
transcript LOC_Os03g63710.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 4
gttgttattgctagcatgttcttattatatcaaatagttttccgcttg-tagattttt-gttatgttaataagtact--gacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGAAGAGAAAGACGCTC
      |  |  |  ||  |   |||||    ||   |||| | |  |  ||||||   | ||  ||  || || ||  ||| || ||  |   | | || |||||| |||| ||||| |||||||||||||||||||||||||| ||||||||||| ||||||||||||||||| | ||||| ||||||||||||||| ||||
---agaaaggtaaatattgtgcaattatgctgaaatatttttcaccggacagatttccagctactttgttatgtgctctgactctagat-tcttttctttacagATTGAGGAAACTGATGAAGCAAGGAAAAAATTCTCTAATGCTAAGGCAATTTCGTCATCTCAGTTTTTTGGTACTCAAAACAGAGAAGAGAAAGAGGCTC

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G176612_T01 (Zea mays), 3'ss of exon 4
-gttgttattgctagcatgttcttattatatcaaatagttttccgcttgtagattttt-gttatgttaataagtact--gacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGAAGAGAAAGACGCTC
    || | |  |  ||     |||||   | |||||| ||||  |    ||||||   ||||  ||  || || ||  ||| || | ||    | | |  ||| || |||| ||||| ||||||||||| |||||||||||||| ||||| || || ||||||||||||||||| | ||||| ||||||||||||||| ||||
taaggtaaatagtgccacaa--ttattgc-tgaaatagctttcatcagccagatttccagttactttgttacgtgctctgactctcggcgcttct-cttcccagGTTGAGGAAACTGATGAAGCAAGGAAGAAATTCTCTAATGCCAAGGCGATCTCGTCATCTCAGTTTTTTGGTACTCAAAACAGAGAAGAGAAAGAAGCTC

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 5
gttgttattgctagcatgttcttattatatcaaatagttttccgcttgt--agatttttgttatgttaataagtactgacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGAAGAGAAAGACGCTC
 | | | | || |     |   ||  | ||| | | | |||    || |  |||  ||  ||        |     |    ||   | |   || |  | |||||||||| |||||||||||||| |  || ||||| ||||| ||  | ||||| |||||||| ||||||||  |||| | || ||  |   | |  | | 
atagatgtggccaat-catctataaaacatctacttggttttttttttttaagaaattcatttaacctgcaccatattttgctttgc-tatgtatccataagATTCAGGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCTCAATTTTTTGGAGATCAGAACAAAGCTGCAGATGTGGATT

upper sequence: LOC_Os03g63710.2 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G12340.3 (Glycine max), 3'ss of exon 4
gttgttattgctagcatgttcttattatatcaaatagttttccgcttgt--agatttttgttatgttaataagtactgacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGA---AGAGAAAGACGCTC---
       | || |     |   ||  | ||| | | | |||    || |  |||  ||  ||        |     |    ||   | |   || |  | |||||||||| |||||||||||||| |  || ||||| ||||| ||  | ||||| |||||||| ||||||||  |||| | || ||    |||    ||  |||   
------gtggccaat-catctataaaacatctacttggttttttttttttaagaaattcatttaacctgcaccatattttgctttgc-tatgtatccataagattcagGAAACTGACGAAGCAAGAAGGAAGTTCTCAAATGCTAAATCTATTTCTTCATCTCAATTTTTTGGAGATCAGAACAAAGCTGCAGATGTGGATTCTCAAG

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|38476645|gb|CF960778.1|CF960778
EST:     TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAG                         ATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
genomic: TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAGgtaaatattg ... tacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
EST: gi|86592535|gb|CI253216.1|CI253216
EST:     TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAG                         ATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
genomic: TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAGgtaaatattg ... tacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
EST: gi|66922735|gb|CX109583.1|CX109583
EST:     TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAG                         ATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
genomic: TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAGgtaaatattg ... tacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
EST: gi|29645174|gb|CB650181.1|CB650181
EST:     TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAG                         ATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
genomic: TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAGgtaaatattg ... tacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
EST: gi|86859205|gb|CI277095.1|CI277095
EST:     TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAG                         ATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
genomic: TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAGgtaaatattg ... tacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
EST: gi|29677840|gb|CB674115.1|CB674115
EST:     TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAG                         ATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT
genomic: TGGATAATGGGTTCCAAAAGAAAACAAGCACAGCTGCCACAAAGACCCAGgtaaatattg ... tacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgtagatttttgttatgttaataagtactgacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGAAGAGAAAGACGCTC
                          tactgac  putative branch site (score: 1)
                                             tacctttc  putative PPT
      atttttgttatgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgttattgctagcatgttcttattatatcaaatagttttccgcttgtagatttttgttatgttaataagtactgacactggacgtgaatacctttcagATTCAGGAGACTGACGAAGCAAGGAAAAAATTCTCTAATGCAAAGGCAATTTCATCATCTCAGTTTTTTGGCAATCAAAGCAGAGAAGAGAAAGACGCTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - -tattgct
- - - - - - - catgttc
- - - - - - - - - - - - - - - - - - - - - -gcttgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctggacg