ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA

Basic information

species	Oryza sativa
transcript	LOC_Os06g46310.1
intron #	6
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069198_T05 (Zea mays), 3'ss of exon 6

tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
| | ||  |    |    |  | ||| | |   || |  |||| || ||| ||   ||    ||  || | || |    ||||  | ||  |||||  |||||||||||||||||||||| | |||||||| || | |||||| || |||||||||||||| |||||||||||||||||||| |||||  | || || ||
tgtctgtcaaactagcagatcacacaaccgattcttttagctttatgttgaattctccagtaatttcttatcaactaagatggcggtttactctttgtagTAATTGGAACTGCTTTTGCTCTAAACATGCTGTTCAGAATCCCAGTATGGTGTGGTGTTCTAATAACTGGACTCAGCACTCTAATGCTCTTATTGCTGCA

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G069198_T04 (Zea mays), 3'ss of exon 6

tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA----------
                                    || |||| || ||| ||   ||    ||  || | || |    ||||  | ||  |||||  |||||||||||||||||||||| | |||||||| || | |||||| || |||||||||||||| |||||||||||||||||||| |||||  | || || ||          
------------------------------------ta-gctttatgttgaattctccagtaatttcttatcaactaagatggcggtttactctttgtagtaattggaactgcttttgctctaaacatgctgttcagAATCCCAGTATGGTGTGGTGTTCTAATAACTGGACTCAGCACTCTAATGCTCTTATTGCTGCAGCAATATGGG

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA15G00590.1 (Glycine max), 3'ss of exon 5

tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctcca-tggttgcttgttctttt-cagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
     | |    |||  ||| | |  | | ||  | | |  |    |||   | || |  ||||   |    | | |  | |  ||  |||| |   | |||||||||| || || ||||| |||||||||||||| || || ||||| |||  |||||||||  | || |||||||||||  |||| ||  |   | ||||
--ctagtttttaaaacaaaccataactttccatttcttttttctgcattctctttaacttctatttatcttaatcttgaaattttttattgtacacatgcagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATCCTCTTAGCATTACA

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: GLYMA13G44710.1 (Glycine max), 3'ss of exon 4

tttgtgatagggaaaataacaagacatctgcaactatatgcttcatattgcatctacccactatacctaaccagcctccatggttgc--ttgttctttt-cagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
     | |    |||  ||||  || | | ||  | | |  |    |||   | || |   |||   |    | | |  ||  ||    |||| |   | |||||||||| || || ||||| |||||||||||||| || || ||||| |||  |||||||||  | || |||||||||||  |||||||  |   | | ||
--ctaggttttaaaacaaacataac-tttccatttcttttttctgcattctctttaacttttatttatcttaatcttgaatttttttcattgtacacatacagTAATTGGGACAGCCTTTGCATTGAACATGCTCTTCAACATACCTGTTTGGATTGGTGTTCTTCTGACAGGACTCAGCACATTGATGCTCTTAGCATTGCA

upper sequence: LOC_Os06g46310.3 (Oryza sativa), 3'ss of exon 6
lower sequence: Vv09s0070g00210.t01 (Vitis vinifera), 3'ss of exon 6

tttgtgatagggaaaataacaagacatctgca--actatatgcttcatattgcatctacccactat--acctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA
 |  || |     || |  ||     ||| ||  | |||   ||| || |  |||  ||      |  |||||  | |  | | ||  || ||  | ||| |||| |||||||| || ||||| |||||||||||||| || || ||||||||||||||||||||  | || || || || ||  || | || ||     ||||
-taatggtttcttaagtg-catcctctcttcattattattaacttgatgtgtcatgcacatttcttcaacctattctgatttc-tgcatgttt-ctttttccagTGATTGGAACAGCCTTTGCATTGAACATGCTCTTCAATATTCCTGTGTGGTGTGGTGTTCTTCTTACAGGGCTTAGTACATTGGTTCTTCTAGCTTTACA

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|33653430|gb|CF276044.1|CF276044

EST:     ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAG                         TAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAA-TCCCTG
genomic: ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAGgtaccagagt ... ttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTG

EST: gi|29664628|gb|CB660903.1|CB660903

EST:     ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAG                         TAATTGGAACTGCTTATGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGT
genomic: ATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAGgtaccagagt ... ttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGT

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: 70 (upstream exon), 62 (downstream exon)
Score: 14

CACCTGGCCGAGCATTGCAGAGCTGAATATCCAAAGGCTACAAATTTCATATTATGGATTCTTGCGGAACTAGCTGTAGTTGCATGCGACATTCCTGAAGgtaccagagt ... ttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tattgcatctacccactatacctaaccagcctccatggttgcttgttcttttcagTAATTGGAACTGCTTTTGCTTTGAACATGCTCTTTAAAATCCCTGTGTGGTGTGGTGTTCTGATAACTGGACTCAGCACTCTGATGCTACTGTTACTACA