ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtagcaaggcagctcttattttattctctataataatcacgtactattccatcatttatctctaaatgatagcttcttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAATCACTTATGTACTTGTGGCGTCTTACGGGGAACAAAACATACCAAGACT

Basic information

species	Oryza sativa
transcript	LOC_Os04g51690.1
intron #	12
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G128914_T01 (Zea mays), 3'ss of exon 12

gtagcaaggcagctctt-attttattctct----ataataatcacgtactattccatcatttatctctaaatgatagcttcttaatt----tagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAATCACTTATGTACTTGTGGCGTCTTACGGGGAACAAAACATACCAAGACT
|||| | |||| | ||| ||||| | ||||    |||||||  |  |  ||    | |||  || ||| |||| ||  ||| || |     ||||| ||||  ||||||||||| ||||| ||| ||||||| |||||||| ||||||||||||||| | |||||  | |||||||| | |||||||||||| |
gtagtatggcacccctttattttttcctcttccaataataaaaatcttgtaccaaaccatcaat-tctgaatgttattttcctactaagcatagGACATGAGTGTGGGCACATCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTTATGTACCTATGGCGCTTGACGGGGAATACAACATACCAAGATT

upper sequence: LOC_Os04g51690.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G130889_T01 (Zea mays), 3'ss of exon 13

gtagcaaggcagctcttattttattctctat-aataatcacgtactattccatcatttatctctaaatgatagcttcttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAATCACTTATGTACTTGTGGCGTCTTACGGGGAACAAAACATACCAAGACT
|||| | | || | |||  ||| | |||| | |||||| |    ||  ||||      | |  | |||  |  || || | | ||||| |||   |||||||| || ||||| ||| ||||||| |||||||| |||||||| |||||| |||||||  | |||||||| |||||||||||||| |
gtagtatgacaaccctttatttttcctctttcaataataaaaatcttgtcca------aaccatcaat--ttcctactgactatagGACATGGGTGTGGGCACGTCGTGGAACATCTTGAGACCGGAGACTGTTGAATCACTGATGTACCTGTGGCGCTTGACGGGGAATAAAACATACCAAGATT

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|58689182|gb|CK077869.1|CK077869

EST:     CAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG                         GATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAA
genomic: CAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAGgtagcaaggc ... cttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAA

EST: gi|218493252|gb|FG945787.1|FG945787

EST:     CAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAG                         GATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAA
genomic: CAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAGgtagcaaggc ... cttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAA

EST: gi|25802227|gb|CA758188.1|CA758188

EST:     AACTCCTACAAATGT-GGCTGGGGAGAATTATTTTTTCCATACTGGACAG                         GATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAA
genomic: AACTCCTACAAA-GTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAGgtagcaaggc ... cttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAA

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: 49 (upstream exon), 48 (downstream exon)
Score: 11

CTTGCTCGGACCTGTTATAACTTCTACCAAACAACTCCTACAAAGTTGGCTGGGGAGAATTATTTTTTCCATACTGGACAGgtagcaaggc ... cttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAATCACTTATGTACTTGTGGCGTCTTACGGGGAACAAAACATACCAAGACT

<

<

<

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taataatcacgtactattccatcatttatctctaaatgatagcttcttaatttagGATATGAACGTGGGCACATCATGGAATATCCTGAGACCTGAGACTGTCGAATCACTTATGTACTTGTGGCGTCTTACGGGGAACAAAACATACCAAGACT