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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaaatattcttcactgtgatagttcagttaatgatattttttgacgcatctaagagatcacattcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTGGTTCTAGAACATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGT

Basic information

species Oryza sativa
transcript LOC_Os01g72340.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g72340.2 (Oryza sativa), 3'ss of exon 10
lower sequence: GRMZM2G032496_T01 (Zea mays), 3'ss of exon 2
gtaaaatattcttcactgtgatagttcagttaatgatattttttgacgcatctaagagatcacattcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTGGTTCTAGAACATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGT
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gtaaaatattcttacctgt--cagtttaatttctg-tacttct-----catctaatgg-taacattcttctagGTTGGATTCGTGAAAGGGATCCAACAAGACTCCTCCATTATGAGGGAGGTGGTTCCAGAACATCATCCACAGATATTGTGTGCCCCATGTATATGCGTGT
















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|58692909|gb|CK081596.1|CK081596
EST:     GTCCTTGGGAAATGAATCTTCGTATGGACCAAATCACTCAGCCATGTCTG                         GCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTG
genomic: GTCCTTGGGAAATGAATCTTCGTATGGACCAAATCACTCAGCCATGTCTGgtaaaatatt ... attcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTG
EST: gi|38568808|gb|CD671023.1|CD671023
EST:     GGGAAATGAATCTTCGTATGGACCAAATCACTCAGCCATGTCTG                         GCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTG
genomic: GGGAAATGAATCTTCGTATGGACCAAATCACTCAGCCATGTCTGgtaaaatatt ... attcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTG
EST: gi|29657376|gb|CB653651.1|CB653651
EST:     GTCCTTGGGAAATGAATCTTCGTATGGACCAAATCACTCAGCCATGTCTG                         GCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTG
genomic: GTCCTTGGGAAATGAATCTTCGTATGGACCAAATCACTCAGCCATGTCTGgtaaaatatt ... attcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTG

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: 70 (upstream exon), 75 (downstream exon)
Score: 21

GTTGTTGGTATGGTGGAGAGAGACAAGAATCATGCATGCATTATAGTATGGTCCTTGGGAAATGAATCTTCGTATGGACCAAATCACTCAGCCATGTCTGgtaaaatatt ... attcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTGGTTCTAGAACATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatagttcagttaatgatattttttgacgcatctaagagatcacattcttgtagGCTGGATTCGTGGAAAGGACCCGACAAGGCCCATCCATTATGAAGGAGGTGGTTCTAGAACATCCTCCACTGATATTGTATGCCCAATGTACATGCGTGT
                      ttttgac  putative branch site (score: 21)
 cattctt  putative PPT
 agttaatgatattttt  TA-rich tract