ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT

Basic information

species	Oryza sativa
transcript	LOC_Os01g43150.1
intron #	10
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 10

-----gtaaccttatcacat-atttaacagtccatcacacagaggactttatgtaaattgtgttttctattgatttt-------gcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
     |  |   |||||  | ||  || || |||    ||  || ||||||| | | |  || || | |||||| ||        ||||||||||||||||||||||| |||||||||||||| ||||||||||| ||||| ||||||||||||||||| |||||||||
gcaatgctagtctatcatgtgatcgaatagaccaatgtactcagaactttatctgactcttgcttccaattgatcttttatctcacagGGAATAATTGTGATGGCTGCAACAAACTTGCCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 10

----gtaaccttatcacat-atttaacagtccatcacacagaggactttatgtaaattgtgttttctattgatttt-------gcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
    |  |   |||||||| ||  || ||  ||  | |   || ||||||  | | |  || || | |||||| ||        ||||||||||||||||||||||| ||||||||| |||| ||||||||||| ||||| ||||||||||||||||| |||||||||
gtatgctagtctatcacattatcaaatagagcaatatattcagaactttacctgactcttgcttccaattgatcttttatcttacagGGAATAATTGTGATGGCTGCAACAAACTTGGCAGACATTCTTGATCCTGCACTCACAAGACCTGGTAGATTTGATAGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA14G29810.1 (Glycine max), 3'ss of exon 2

gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
||| | ||   |||  ||  |  |    ||   |    |  ||||   ||||||  |  |   || || ||| ||||||||||  |||||||||| ||||||||||| ||||||||||| |||||  | || || ||||| ||||| ||| |||||
gtatctttga-acagtttggagtgcaattcgttcctctggttttag--aaattgattcattattttatcttgtagGGAATAATATTGATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACTAGGCCTGGAAGATTTGATCGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA13G08160.1 (Glycine max), 3'ss of exon 10

gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
||| | ||   |||  ||  |  |    |    |    |  ||||   ||||||  |  |   || || ||  ||||||||||  | |||||||| ||||||||||| ||||||||||| |||||  | || || ||||| ||||| ||| |||||
gtatctttga-acagcttggagtgcaatttgttcctctggttttag--aaattgattcattattttatcttctagGGAATAATATTAATGGCTGCAACAAACTTGCCTGATATTCTTGACCCAGCTTTAACGAGGCCTGGCAGATTTGATCGGCAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: GLYMA06G13140.1 (Glycine max), 3'ss of exon 10

-------gtaaccttatcacatatttaacagtccatcacacagaggact-ttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
         ||  ||   |||| | | |  ||  |            || ||   ||| || |      | || || ||| |||||||||| || || ||||| |||||| |||| |||||||||||||| ||  | ||||| ||||||||||| ||||| |||
gtatatttcaagttttaaacatttgtgagtgtttaattagtttctctctgtttcctaatttattcaacatctttatcttgtagGGAATAATAGTAATTGCTGCAACAAACCTGCCTGATATTCTTGATCCCGCTTTAACAAGGCCTGGTAGATTTGATAGACAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 10

-----------------gtaaccttatcacatatttaacagtccatcacacagaggactttatgtaaattgtgttttctatt--gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
                 |||   | |||   |  ||| |   |  |       |||| | ||     | | || ||||||||  | || ||||||||||||| || |||||||| ||||||||||| ||||| ||||||||||| || |||||||| |||||||| ||||| |||
gtacttgttgattaggagtagtgt-atcttgtgatta-cttccgctagtttgcaggaatataatagtactttgctttctattttggttatgcagGGAATAATAGTTATGGCTGCAACAAACTTGCCTGATATACTTGATCCAGCTCTGACAAGACCGGGTAGATTTGATAGACAT

upper sequence: LOC_Os01g43150.2 (Oryza sativa), 3'ss of exon 2
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 10

gtaaccttatcacatattt-----aacagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT
||||| |    ||| | ||     |  |||  ||        | | ||| | ||| |||  |  |  |||  | ||| |||| |||||  ||||||| || ||||||||||| |||||||||||||||||  | ||||||||||||||||| || ||||||
gtaacatatggacaaacttgtgttattagtgaatatttttctgcatttt-tttaacttggataat--atttttcttgtagGGCATAATATTGATGGCAGCAACAAACTTGCCTGATATTCTTGATCCAGCTTTAACAAGACCTGGTAGATTTGACAGGCAT

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|88369682|gb|CI582877.1|CI582877

EST:     GGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: GGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA

EST: gi|51946127|gb|CV152468.1|CV152468

EST:     CTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: CTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA

EST: gi|29682022|gb|CB678297.1|CB678297

EST:     AAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAG                         GGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA
genomic: AAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCA

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: 62 (upstream exon), 51 (downstream exon)
Score: 33

AATAGATGCTGTGGGTTCAACTAGAAAACAGTGGGAAGGACACACAAAGAAAACATTGCATCAACTTCTTGTCGAGATGGATGGTTTTGAACAAAATGAGgtaaccttat ... gattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

acagtccatcacacagaggactttatgtaaattgtgttttctattgattttgcagGGAATAATTGTGATGGCTGCGACAAACTTGCCAGATATTCTTGATCCAGCACTTACAAGACCTGGTAGATTCGATAGGCAT