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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcttcagtatgccatagaacacactcgcatcgactggaaatatcgagcaattcttcctaatataaggtaactgattgtctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCCAGAGAAGGATCGATATTACTCCACTAGGGGTTCTCCATTCCCATTCGAG

Basic information

species Oryza sativa
transcript LOC_Os03g59250.1
intron # 2
splice site 3'
intron type U2

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|33799308|gb|CF325510.1|CF325510
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
EST: gi|58665713|gb|CK054399.1|CK054399
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
EST: gi|88973688|gb|CI718116.1|CI718116
EST:     GATGTTGCCCCGTTTCGTTCGCCGNGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGAT
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGAT
EST: gi|88316424|gb|CI621663.1|CI621663
EST:     GATGTTGCCCCGTTTCGTTCGCCGTGGCGCCCGAGCACGCTGAAGCGAAG                         GAAAACCGAGGCATTTGTGAGCGATAACAGG
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGG
EST: gi|13165451|gb|AU174248.1|AU174248
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
EST: gi|66924161|gb|CX111009.1|CX111009
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
EST: gi|58675936|gb|CK064623.1|CK064623
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
EST: gi|58656489|gb|CK045169.1|CK045169
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCC
EST: gi|88669289|gb|CI719427.1|CI719427
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCANGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAAC
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAAC
EST: gi|86902195|gb|CI302226.1|CI302226
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGA
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGA
EST: gi|88672278|gb|CI726394.1|CI726394
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAG
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAG
EST: gi|88667193|gb|CI719329.1|CI719329
EST:     GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAG                         GAAAACCGAGCCATTTGTGAGCGATAACAGGCA
genomic: GATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCA

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: 65 (upstream exon), 68 (downstream exon)
Score: 5

CCGATGTTCTTAGGCGCACCATACCACGAGTGAATCGCCCGCTTGGCGGTGATGTTGCCCCGTTTCGTTCGCCGCGGCGCCCGAGCACGCTGAACCGAAGgtagcttcag ... ctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCCAGAGAAGGATCGATATTACTCCACTAGGGGTTCTCCATTCCCATTCGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctggaaatatcgagcaattcttcctaatataaggtaactgattgtctgagagcagGAAAACCGAGCCATTTGTGAGCGATAACAGGCACTCCATGTCACTCTCGCCAGAGAAGGATCGATATTACTCCACTAGGGGTTCTCCATTCCCATTCGAG
                        taatataa  TA-rich tract