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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTGGTGAAGCATGAAGGGTGGGAGCGGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcgttttgctgatcgattttcaccagcttccctgccttgttggaggattagctgtaccagcttctgaatcgaatcattgtgtctgtag

Basic information

species Oryza sativa
transcript LOC_Os03g15860.1
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g15860.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G540403_T02 (Zea mays), 5'ss of exon 3
GTGGTGAAGCATGAAGGGTGGGAGCGGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcgttttgctgatcgattttcaccagcttccctgccttgttggaggattagctgtaccagcttctgaatcg--aatcattgtgt--ctgtag-
|| |||||| | || ||||||||||| ||||| ||||| || |||||||| || || ||||| || ||||||||||||| ||                  ||| ||||||||  | ||   || | | |   | ||   | |||||||||||     || ||||||  ||||   
GTTGTGAAGAACGAGGGGTGGGAGCGCCTGTATGGCGGGCTTATGCCCTCTCTCGTCGGCACCGCTGCCTCCCAGgttggttca----------------ttcgccagcttcgttccccactttgtgaa--ggttgagac-gcttctgaatctttgctcgttgtgttactgtcag
















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|88764015|gb|CI773431.1|CI773431
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
EST: gi|33682306|gb|CF310545.1|CF310545
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCATATAT
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATAT
EST: gi|88733492|gb|CI756669.1|CI756669
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCC
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCC
EST: gi|88336258|gb|CI648845.1|CI648845
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
EST: gi|29636135|gb|CB641144.1|CB641144
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
EST: gi|33691776|gb|CF320015.1|CF320015
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
EST: gi|29636132|gb|CB641141.1|CB641141
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
EST: gi|88361286|gb|CI626390.1|CI626390
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGACTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
EST: gi|117244127|gb|CT848393.1|CT848393
EST:     GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAG                         GGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG
genomic: GGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCG

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

GTGGTGAAGCATGAAGGGTGGGAGCGGCTGTACGGCGGCCTCATGCCCTCGCTTGTTGGCACTGCGGCCTCCCAGgttgctttcg ... gtgtctgtagGGTGTCTACTATTACTTCTACCAGATATTCCGGAGCAGGGCGGAGGCCGCGGCTCTCCAGCGATCCAGGAGAGGAATCGGCGATGGATCCGTCGGGATGC




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