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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatcatcagctcagatcgttggcgaatttcggctttgatttttggtcgctgctgatatagatgcgaactaatttgggtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCA

Basic information

species Oryza sativa
transcript LOC_Os01g07720.3
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07720.4 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G066362_T02 (Zea mays), 3'ss of exon 2
----------------------------------gtatcatcagctcagatcgttggcgaatttcggctttgatttttggtcgctgctgatatagatgcgaactaatttggg-----tgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCA
                                  || ||  | |||    | |||   || |||||  ||||   |   |  |         | |  |    ||  | || |     ||||  | ||||||||| ||| |||| ||||||||||| ||||||||||||||||| ||||| |||||  | |||||||||||||| ||||||||||| ||||||||| 
gtgctagcgcaattggggagcctttttttttatcgtttcccc-gctgttttggttcaagagtttcgaatttgggatggtggtgtgatcttggttggcggctgctggtgtgtgcttcctgcgcta-gGTGGACGCTTTTCTGGAGGGGGAGAGGGACTACACCAAGATCGAGGGAGACACAGGGCCATTGGTCTACCCGGCCGGATTCCTCTACGTCTACTCCGCCG
















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|88368729|gb|CI645151.1|CI645151
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTNTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88740960|gb|CI764468.1|CI764468
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATAACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88765491|gb|CI774585.1|CI774585
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88734598|gb|CI758106.1|CI758106
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88312323|gb|CI582661.1|CI582661
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88576279|gb|CI670424.1|CI670424
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88309854|gb|CI656988.1|CI656988
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88763364|gb|CI772825.1|CI772825
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88592824|gb|CI710953.1|CI710953
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88449328|gb|CI582200.1|CI582200
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88327935|gb|CI648334.1|CI648334
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88763578|gb|CI773025.1|CI773025
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88741433|gb|CI764941.1|CI764941
EST:     ATACCAAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|87008978|gb|CI304921.1|CI304921
EST:     ATACCAAGATCGACTGGGACGCGTACATAGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
EST: gi|88337341|gb|CI629631.1|CI629631
EST:     ATTAC-AAGATCGACTGGGACGCGTACATGGCTCAG                         GTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC
genomic: AT-ACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGAC

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), 68 (downstream exon)
Score: 13

ATACCAAGATCGACTGGGACGCGTACATGGCTCAGgtatcatcag ... gtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctttgatttttggtcgctgctgatatagatgcgaactaatttgggtgcgagaagGTGGACGCGTTTGTGGAAGGGGAGAGGGATTACACCAAGATCGAGGGCGACACGGGGCCGCTCGTCTACCCGGCCGGCTTCCTCTACGTTTACTCCGCCA
                                  aactaat  putative branch site (score: 13)
                                  aactaattt  TA-rich tract