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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtattctatttgctaggcaggctcattcacttagtcatgctgttttagtccgtacatagggattcatttttaactcaactgcttttttgcttgggcagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG

Basic information

species Oryza sativa
transcript LOC_Os07g22720.1
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G015132_T01 (Zea mays), 3'ss of exon 16
---atgtattctatttgctagg-caggctcattcacttagtcatgctgttttagtccgtacatagggattcatttttaactcaactgcttttttgcttgggcagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG
    |    | ||||||||    |||  |  || | | | || |  | ||     | |  | ||  | |   |  ||   | || ||| || ||  ||| |||||||||| |||||||||||||||   |||  |||| || |  || |||||||| |||||||| || ||| |||||||||| ||||||||||| ||||
tttctactctatatttgctccttcagaatggtttaataaatccttgttttgctagcagctcttaatgttctttcattg--ttaattgcattctt--ttgtgcagCTGAGAAGAGGGTGATACCTGGTTCCGCTGATGGCCAGTTTGAATTTGGTTCATTCATGTCAGCTACACTGAGCTGTGACCACAGGGTTATAGATG

upper sequence: LOC_Os07g22720.1 (Oryza sativa), 3'ss of exon 17
lower sequence: GRMZM2G161969_T01 (Zea mays), 3'ss of exon 13
-------------------------------------------------atgtattctatttgctaggcaggctcattcactt--agtcatgct-gttttagtccgtacatagggattcatttttaactcaactgcttttttgcttggg---cagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG
                                                 | | ||    |  | |  | |      || | ||  ||||||  | |   ||     ||  |||||  |     ||   | ||   |  ||| | |       ||            |||||||||||   |||| ||||||  || ||||||||||| |||||||| || ||| |||||||||| ||||||||||| ||||
gtgatacctagggctgacaatgggctgtaaattttacactataagatttaaggatcgagtcgggttaggatcgggctttatttcaagtcatttttgaactataatttatttagggccttgacattttgtgaagaaccatttggatcacaatccattaccacccttagTGATACCTGGTTCCGCCGATGGTCTGTATGAGTTTGGTTCGTTCATGTCAGCCACACTGAGCTGTGACCACAGGGTTATAGATG
















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|86477689|gb|CI120322.1|CI120322
EST:     TTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTTCTG                         CTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTT
genomic: TTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTTCTGgtaataagtc ... gcttgggcagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTT
EST: gi|89192614|gb|CI049912.1|CI049912
EST:     TTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTTCTG                         CTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTT
genomic: TTGTGCCATCATAAATCCTCCTCAGTCGGCAATCTTGGCCATTGGTTCTGgtaataagtc ... gcttgggcagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttagtccgtacatagggattcatttttaactcaactgcttttttgcttgggcagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG
                        ttttaac  putative branch site (score: 2)
                                   ctgcttttttgctt  putative PPT
                  attcatttttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtattctatttgctaggcaggctcattcacttagtcatgctgttttagtccgtacatagggattcatttttaactcaactgcttttttgcttgggcagCTGAGAGGAGGGTGATACCTGGCAGCGCCAATGGTCAATACGAGTTTGGTTCCTTCATGTCGGCAACAATGAGCTGTGATCACAGGGTTATTGATG

- - - - - tttgcta
- - - - - - - - -ggcaggc
- - - - - - - - - - - - -cattcac
- - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -ccgtaca