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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggcttgtctgctctttctctgatacatactttttctgtaaattttgagcattttgatctcagccgcttttgtttctctgttttcagGCCAGGGCTATGGGGAAATGAAG

Basic information

species Oryza sativa
transcript LOC_Os07g04990.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g04990.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT1G06690.1 (Arabidopsis thaliana), 3'ss of exon 4
gtcggcttgtctgctctttctctgatacatactttt-tctgtaaattttgagcattttgatctcagccgcttttgtttctctgttttcagGCCAGGGCTATGGGGAAATGAAG
        || ||| |   | || || |||  |    |    ||   | ||   |    ||||||  |  |||| ||  |    |||||||||||| ||||||||||||||||
--------gtatgcac---ccctaattcatgttggagtaaacaacactagaaggtaacaatctca--ctattttcttaattatatttcagGCCAGGACTATGGGGAAATGAAG
















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|38478740|gb|CF962873.1|CF962873
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|88368695|gb|CI675516.1|CI675516
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|313083769|gb|HO213899.1|HO213899
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|95101321|gb|CI693066.1|CI693066
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|58586534|gb|CF984842.1|CF984842
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|58605103|gb|CK033136.1|CK033136
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|58592358|gb|CF990666.1|CF990666
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCANGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|29684749|gb|CB681024.1|CB681024
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|313080415|gb|HO213423.1|HO213423
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|29685611|gb|CB681886.1|CB681886
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|29685612|gb|CB681887.1|CB681887
EST:     CAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: CAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|38483088|gb|CF966890.1|CF966890
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|58589665|gb|CF987973.1|CF987973
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCANGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG
EST: gi|38480259|gb|CF964348.1|CF964348
EST:     TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTG                         GCCAGGGCTATGGGGAAATGAAG
genomic: TCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG

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), 23 (downstream exon)
Score: 74

CACTTCCATGGAGATTTGGCCGAGGAAGTGTTCTTTCCGCACTGAAGAAATCGCTTGACCGTCTTGGGTTATCTTCAGTTGAGCTCTACCAACTTCATTGgtcggcttgt ... ctgttttcagGCCAGGGCTATGGGGAAATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttctgtaaattttgagcattttgatctcagccgcttttgtttctctgttttcagGCCAGGGCTATGGGGAAATGAAG
                   ttttgat  putative branch site (score: 74)
                               ccgcttttgtttctct  putative PPT
      taaattttga  TA-rich tract