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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtccatggccttccatttcatgaccaatattttctgaaacttggcaagaaggtttgatgaaatttttttttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCATCCAGCCATGGGATTCTTGCACAATAACAA

Basic information

species Oryza sativa
transcript LOC_Os10g40140.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G074173_T01 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------gtccatggccttccatttcatgaccaatattttctgaaa--cttggcaagaag-gtttgatgaaatttttt--------tttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCATCCAGCCATGGGATTCTTGCACAATAACAA
                                                                       ||| | |       ||  || |  |        ||||  ||   | ||    | ||| ||||||||           ||||||||||| ||||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||||||| |
gtccgtagcttcggctatcgcattcgcgtgatgttcgcctcagaatttccgcgttttttgcttgctggaaaccaagccaggtggcttggtgtctgaggggagaagaaaaactaaactaggtctggttggtgaaatttgcccgattcactttcagGTCAAAACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA

upper sequence: LOC_Os10g40140.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G171406_T06 (Zea mays), 3'ss of exon 2
--------------------------------------------------gtccatggccttccatttcatgaccaatatttt--ctgaaacttggcaaga--aggtttgatgaaattt--------ttttttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCATCCAGCCATGGGATTCTTGCACAATAACAA
                                                  |  |   |     |    || |    || ||        ||     | |||  |||| || | ||||||        | |||||||||||| || ||||| |||||||||||||| ||||||||||||||||||||| |||||||||||||||||||||||||||| |
gtccatgtcttccctgtcccgtgaagttcacctcagaatctccgcgttttgctcgctgaaaatcgaaccaggtttgatgttgagatgagaagaaaactagactaggtctggtcaaatttgccccatttattttcagGTCAAAACAACATCGCCGAGGAAGTATTTCGTCCGGCCGAACGCGAGCATCGTCCAGCCATGGGATTCTTGCACAATAACGA
















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|88400668|gb|CI596089.1|CI596089
EST:     ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAG                         GTCAAGACGAGATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATC
genomic: ATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAGgtccatggcc ... tttttttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATC




















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: 27 (upstream exon), 48 (downstream exon)
Score: 5

TTGAGCTAGATAAGCCATGCTATTGCAATCTCAAGGTGGTGAACAACAGCGAGCATCATGTTGCATTTAAGgtccatggcc ... tttttttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCATCCAGCCATGGGATTCTTGCACAATAACAA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaccaatattttctgaaacttggcaagaaggtttgatgaaatttttttttcagGTCAAGACGACATCACCGAGGAAGTATTTTGTCCGGCCGAACGCGAGCATCATCCAGCCATGGGATTCTTGCACAATAACAA
                                gtttgat  putative branch site (score: 5)
                                           tttttttttc  putative PPT
                                 tttgatgaaatttttt  TA-rich tract