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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaaagatgaacctagattcatcagtagtgtcacttttcaagtatatatatttgtcgacatctttgcatatcctgcttgatcacttcattcgctaccttcaatttcaaaaaactgcagGTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATAG

Basic information

species Oryza sativa
transcript LOC_Os03g24460.2
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 11
lower sequence: GRMZM2G108416_T01 (Zea mays), 3'ss of exon 11
gtaaaaagatgaacctagattcatcagtagtgtcacttttcaagtatatatatttgtcgacatctttgc-atatcctgcttgatcacttcattcgctaccttcaatttca---aaaaactgcagGTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATAG
||||||  ||  | | ||||||||||  | ||||||| ||  | |||  |||| | ||  | || |  | |  |  |   | ||  | ||||||  | | ||   | | |   |  || || ||||||||||||||||||||||||||||||| || ||||| ||  ||||||| |
gtaaaat-atagatcaagattcatca-caatgtcactattataatatg-atatctatcaccttcataacgaccttatcgctcattgcctcattcaattcattggctgtgatttatcaagtgaagGTGACATCTGGAATGAGTCCAGCTTTCAATCTTTATGGGTGTGCCTTGATTG

upper sequence: LOC_Os03g24460.3 (Oryza sativa), 3'ss of exon 11
lower sequence: PP1S81_64V6.1 (Physcomitrella patens), 3'ss of exon 10
------gtaaaaagatgaacctagattcatcagtagtgtcacttttcaagtatatatatttgtcgacatctt---tgcatatcctgcttgatcacttc----attcgc-taccttcaatttcaaaaaact----gcagGTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATAG
      || |  |  |      |      | |    | |   | |  |  ||||||||| | |  |||||||   | ||    || | | | ||        ||||   | |   || | | |      |    ||||   ||||| ||||||||||||||||| ||| ||||||||||||  || || |
gtagttgtcactatctctggtcaagccatttatatatatatatatatatatatatatatatatgcacatcttgtgtacagtatctacgttagcatccttggaattcctgtgctaacagtgttagtggcttttatgcagACTACATCAGGAATGAGTCCAGCTTTTAACGTCTATGGATGCAATTTAATTG
















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|58665374|gb|CK054060.1|CK054060
EST:     GAATGTTCAATAATGCTCATATAAGGCTTACACTCACCCGTGGGAAGAAG                         GTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATA
genomic: GAATGTTCAATAATGCTCATATAAGGCTTACACTCACCCGTGGGAAGAAGgtaaaaagat ... aaaactgcagGTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATA
EST: gi|29621730|gb|CB626741.1|CB626741
EST:     GAATGTTCAATAATGCTCATATAAGGCTTACACTCACCCGTGGGAAGAAG                         GTGACATCTGGAATGAGTCCAGCTTTCACCCTCTATGGATGCACCTTGATA
genomic: GAATGTTCAATAATGCTCATATAAGGCTTACACTCACCCGTGGGAAGAAGgtaaaaagat ... aaaactgcagGTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATA

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 53 (upstream exon), 50 (downstream exon)
Score: 29

ATTAAGGATGCCATCTTTAGGACTCTCAATGCAAATGGAATGTTCAATAATGCTCATATAAGGCTTACACTCACCCGTGGGAAGAAGgtaaaaagat ... aaaactgcagGTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgcatatcctgcttgatcacttcattcgctaccttcaatttcaaaaaactgcagGTGACATCTGGAATGAGTCCAGCTTTCAACCTCTATGGATGCACCTTGATAG
           gcttgat  putative branch site (score: 29)
                                  ttcaatttcaaaaaa  TA-rich tract