ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAAATTTTAGGGCTCTTTGTACAGgtatttcttcttcctagatctattcctgttacagctgaaattcaaccttctgttcacatgattatccatattgcactctgttcactattgcag

Basic information

species	Oryza sativa
transcript	LOC_Os09g36670.1
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G158237_T05 (Zea mays), 5'ss of exon 3

----------------------------------------------------------------------------CAAATTTTAGGGCTCTTTGTACAGgtatttcttcttcctagatctattcctgttacagctgaaattcaaccttctgttcacatgattatccatattgcactctgttcactattgcag
                                                                             ||| |||||||||||||||||||||||||  ||| |     || ||  ||  |      |  |   | ||  |   | |  ||||  | ||| |  |  | ||||||| ||| |||
TGTAACATATATGAAATAAAATTGGCTTCACAGATTATAGTTCATCTACTAAATTTTTTTGTTCTACACTCTGCAGAAAACTTTAGGGCTCTTTGTACAGgtattttctct-ctggtctccatggcttattttctcgccagcaaccccacc--tgagctgatcgttcatgt--ccatttgttcaccatttcag

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G158237_T01 (Zea mays), 5'ss of exon 4

CAAATTTTAGGGCTCTTTGTACAGgtatttcttcttcctagatctattcctgttacagctgaaattcaaccttctgttcacatgattatccatattgcactctgttcactattgcag
 ||| |||||||||||||||||||||||||  ||| |     || ||  ||  |      |  |   | ||  |   | |  ||||  | ||| |  |  | ||||||| ||| |||
AAAACTTTAGGGCTCTTTGTACAGgtattttctct-ctggtctccatggcttattttctcgccagcaaccccacc--tgagctgatcgttcatgt--ccatttgttcaccatttcag

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G371271_T01 (Zea mays), 5'ss of exon 9

-------------------------------------------CAAATTTTAGGGCTCTTTGTACAGgtatttcttcttcctagatctattcctgttacagctgaaattcaaccttctgttcacatgattatccatattgcactctgttcactattgcag
                                            ||| |||||||||||||||||||||||||  ||| |     || ||  ||  |      |  |   | ||  |   | |  ||||  | ||| |  |  | ||||||| ||| |||
ATTATAGTTCATGTACTAAATTTTTTTGTTCTACACTCTGCAGAAAACTTTAGGGCTCTTTGTACAGgtattttctct-ctggtctccatggcttattttctcgccagcaaccccacc--taagctgatcgttcatgt--ccatttgttcaccatttcag

upper sequence: LOC_Os09g36670.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G086243_T01 (Zea mays), 5'ss of exon 7

CAAATTTTAGGGCTCTTTGTACAGgtatttcttcttcctagatctattcctgttacagctgaaattcaaccttctgttcacatgattatccatattgcactctgttcactattgcag
 ||| |||||||||||||||||||||||||  ||| |     || ||  ||  |      |  |  |||||   | || |  ||||  | ||| |  |  | ||||||| ||| |||
AAAACTTTAGGGCTCTTTGTACAGgtattttctct-ctggtctccatggcttattttctcgccag-caaccccat-ttgagctgatcgttcatgt--ccatttgttcaccatttcag

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|44665422|gb|CR278856.1|CR278856

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA

EST: gi|88570043|gb|CI661218.1|CI661218

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA

EST: gi|88328504|gb|CI676714.1|CI676714

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTA

EST: gi|88580780|gb|CI697732.1|CI697732

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGC
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGC

EST: gi|58601241|gb|CK011769.1|CK011769

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA

EST: gi|87005928|gb|CI289345.1|CI289345

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGAT
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGAT

EST: gi|88307256|gb|CI641892.1|CI641892

EST:     GCCAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA

EST: gi|88580485|gb|CI697419.1|CI697419

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCA

EST: gi|88581910|gb|CI699127.1|CI699127

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGC
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGC

EST: gi|88335390|gb|CI650355.1|CI650355

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATA

EST: gi|58691487|gb|CK080174.1|CK080174

EST:     GCAAATTTTAGGGCTCTTTGTACAG                         GAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA
genomic: GCAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAA

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: 24 (upstream exon), 59 (downstream exon)
Score: 11

CAAATTTTAGGGCTCTTTGTACAGgtatttcttc ... actattgcagGAGAAGAGGGCATTGGGCACAAGGGTAAATCTCTTCACTATAAAGGATCAAGATTTCATCGTATTATCCCAGGCTTCATGATTCAGGGTGGGGACATAGT