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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttcaatggcacactgtacaggaagtataagttctcttttctcatgatcttttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA

Basic information

species Oryza sativa
transcript LOC_Os01g03070.2
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G070487_T04 (Zea mays), 3'ss of exon 4
gtatgttcaatggcacactgtacaggaagtataagttctcttttctcatgatcttttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA
    |||| |   ||   | | |   |  | |  || ||  |||   || ||         ||||  |||   || |     |||  |      |       ||||||||| ||    || || |||||  |||| ||||||||||||||||||||||| || ||||||||||||| |||||| |||||||| ||||||| ||| ||||
----gttcta-atcatgttctgctatatttgtttgtacttattttatataat------tactatttgttg--caataatgacttttagtgtttgtcctcctcttttcagGCCTCTTGTATTTTCCAGTCGATGAAGATTGATATGCTCTCAAGAATGATTCCGTTCTTTGACTTTTTTGTTGTGGAGAAGATTTCTGTTGTTGCTGTGA

upper sequence: LOC_Os01g03070.2 (Oryza sativa), 3'ss of exon 7
lower sequence: GRMZM2G093050_T01 (Zea mays), 3'ss of exon 7
gtatgttcaatggcacactgtacaggaagtataagttctcttttctcatgatcttttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA
                  |    | |   |   |  | | |||   ||| | ||| ||  ||  | | || |  |    ||  || |      | |  | |  |||||||| ||    || ||| | ||  | || ||||||||||||||||||||||| |||||||||||||| ||||| || |||||||| ||||||||||| |  |
--------------gtcttaattaagttctgctatatatgtttgtacataa-cttgtaaattgctatatgttgcaataatgacttctagtgtttctcttccaatttcagGCCTCTTGTATTTTTAAATCCATAAAGATTGATATGCTCTCAAGAATGATTCCATTCTTTGACTTCTCTGTCGTGGAGAAGATTTCTGTTGATGCTGCCA
















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|86427691|gb|CI072788.1|CI072788
EST:     AGTACCTTCCTGCTTNGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|89192877|gb|CI050175.1|CI050175
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|29673992|gb|CB670267.1|CB670267
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAC                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|88964806|gb|CI084804.1|CI084804
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|86429925|gb|CI082348.1|CI082348
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|89185749|gb|CI047618.1|CI047618
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|88263846|gb|CI367620.1|CI367620
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|58695557|gb|CK084244.1|CK084244
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
EST: gi|86432397|gb|CI086008.1|CI086008
EST:     AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCTACAG                         GCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC
genomic: AGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATC

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: 73 (upstream exon), 70 (downstream exon)
Score: 26

TGGAGGGAAGCTTTCATCAGCTCCCTTGGTTCCAGAAGTTTTTCTGTCACAGTACCTTCCTGCTTTGGAGAAGTTAACAACTTTAAGGGTGTTGCAACAGgtatgttcaa ... tctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttacgttattctttggttaacacgtggtttatgcacccttttgttctttttcagGCTTCCCAGATATTTCAGTCTGTGAAAATTGATATGCTCTCAAGAATGATCCCATTCTTTGACTTTTCTGTTGTTGAGAAGATCTCTGTTGATGCCGTGA
               ggttaac  putative branch site (score: 26)
                                tgcacccttttgttct  putative PPT
      ttattcttt  TA-rich tract