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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taatggttctgtttgaaaatttgaatttgtacaccatgtacttatgtcccatttgaaggtgctttctatttactttgcattaattttgtatatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACTCAATGATTATGAAATAGGCCAGAATGAAGTTACTGCTATCAAGGATAAA

Basic information

species Oryza sativa
transcript LOC_Os01g65450.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g65450.1 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G114172_T03 (Zea mays), 3'ss of exon 1
taatggttctgtttgaaaatttgaatttgtacaccatgtacttatgtcc-catttgaaggtgctt-tctatttactttgcattaattttgtatatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACTCAATGATTATGAAATAGGCCAGAATGAAGTTACTGCTATCAAGGATAAA
      ||    | |      ||    ||  ||||   | |   || || |  | ||   || |  | ||| |  |||  | |  | || | ||  |||||| ||  ||||||| ||||||||||| | ||||||||||||||| ||| ||||  | |||| |||  | |  |||||||||| |||  | || |||||||||
--gcccttggagtgggtgccctgttcatgggcaccggctgcacgtgccctcgctcgagcctggtgatttatgtgttttaaagttttcttttctaaatttcagTACAATTGAAGAAGAAATATTTGTCGGCCAAGAAGATGATCCGGAGTTACTTGACGATTTTGACTTTGAGCAGAATGAAGCTACACCCATTAAGGATAAA
















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|58667611|gb|CK056297.1|CK056297
EST:     CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
EST: gi|29685721|gb|CB681996.1|CB681996
EST:     CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
EST: gi|29676775|gb|CB673050.1|CB673050
EST:     CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
EST: gi|88592525|gb|CI710631.1|CI710631
EST:     CTCATCTCCTCCATCCCTTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
EST: gi|396941533|gb|HO188742.1|HO188742
EST:     CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
EST: gi|88588283|gb|CI706090.1|CI706090
EST:     CTCATCTCCTCCATCCCTTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
EST: gi|88721914|gb|CI743426.1|CI743426
EST:     CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGAT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGAT
EST: gi|88433711|gb|CI582033.1|CI582033
EST:     CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACAAAGAAGATGATCCAGAGATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT
EST: gi|88720359|gb|CI743658.1|CI743658
EST:     CTCATCTCCTCCATCCCCTTCAAGCCCAACGTNAAGATCAACATGATCGG                         CACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGACATACT
genomic: CTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACT

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), 74 (downstream exon)
Score: 7

AGAAGCTGCTCTACCCCAAGTTCAAGCTCAACGAGTGCAAGGACTCCGAGCTCATCTCCTCCATCCCCTTCAAGCCCAACGTCAAGATCAACATGATCGGgtaagcgcaa ... tatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACTCAATGATTATGAAATAGGCCAGAATGAAGTTACTGCTATCAAGGATAAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcccatttgaaggtgctttctatttactttgcattaattttgtatatctttcagCACTGTTGAAGATGAAATATTTGTGGACCAAGAAGATGATCCAGAGATACTCAATGATTATGAAATAGGCCAGAATGAAGTTACTGCTATCAAGGATAAA
                                cattaat  putative branch site (score: 7)
                                             tatctttc  putative PPT
                     tatttactttgcatta  TA-rich tract