ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaatttaagcaactcaactgtatgtcttcagcagataattgagtaatgttggatcttcttttgttattctgatatattttaatcttttgcag

Basic information

species	Oryza sativa
transcript	LOC_Os08g40530.2
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G132712_T03 (Zea mays), 5'ss of exon 30

GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaatttaagcaactcaactgtatgtcttcagcagataattgagtaatgttggatcttcttttgttattctgatatatttt-aatcttttgcag
|||||||||||| || ||||| |||||| ||||||||||||| ||||||||                   |||  |||||  | | || ||  |  ||||  |   |||||  || ||||||||| |||  ||| ||   |||
GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttag-------------------tattccttcattatacaactggattctgttaaaaactctttc-ttgttctgatatgtttggaattttacacag

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 14
lower sequence: GRMZM2G309782_T01 (Zea mays), 5'ss of exon 2

GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaatttaagcaactcaactgtatgtcttcagcagataattgagtaatgttggatcttcttttgttattctgatatatttt-aatcttttgcag
|||||||||||| || ||||| |||||| ||||||||||||| ||||||||                   |||  |||||  | | |||||  |  ||||  |   ||||| ||| ||||||||| |||  ||| ||   |||
GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttag-------------------tattccttcattatacaattggattctgttaaaaactcttt-gttgttctgatatgtttggaattttacacag

upper sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 14
lower sequence: AC214484.3_FGT001 (Zea mays), 5'ss of exon 3

GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaatttaagcaactcaactgtatgtcttcagcagataattgagtaatgttggatcttcttttgttattctgatatatttt-aatcttttgcag
|||||||||||| || ||||| |||||| ||||||||||||| ||||||||                   |||  |||||  | | || |   |  | ||  |   ||||| ||| ||||| ||| |||  ||| ||   |||
GGAACCTCTTGTTACAAATATCATGTGGAGAAACTTGTTTGTTCAGgttag-------------------tattccttcattatacaactagattctattaaaaactcttt-gttgttctggtatgtttggaattttacacag

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|29665351|gb|CB661626.1|CB661626

EST:     GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAG                         GCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTGGAAGAAGC
genomic: GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaattt ... tcttttgcagGCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTGGAAGAAGC

EST: gi|29681421|gb|CB677696.1|CB677696

EST:     GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAG                         GCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTG
genomic: GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaattt ... tcttttgcagGCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTG

EST: gi|58690194|gb|CK078881.1|CK078881

EST:     CTTGTTTGTCCAG                         GCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTGGAAGAAGC
genomic: CTTGTTTGTCCAGgttagaattt ... tcttttgcagGCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTGGAAGAAGC

EST: gi|23322134|gb|BU572379.1|BU572379

EST:     CTCTTGTGACTAATATTATGTCGCGAAACTTGTTTGTCCAG                         GCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTGGAAGAAGC
genomic: CTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaattt ... tcttttgcagGCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTGGAAGAAGC

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: 60 (upstream exon), 73 (downstream exon)
Score: 17

GGAACCTCTTGTGACTAATATTATGTGGCGAAACTTGTTTGTCCAGgttagaattt ... tcttttgcagGCCATTTACCAAATAGCGATCCTTCTTATCTTTGATTTTTCTGGAAGAAGCATACTGCGGTTACAGAATGATAGTCGGGAGGATGCTGAGAAAACACAAA