ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

Basic information

species	Oryza sativa
transcript	LOC_Os01g40590.1
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GRMZM2G028037_T02 (Zea mays), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
||| ||||| || ||  |          || ||| |||| |||||| | |       |||       | || | |||||  |||||||||||| || ||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||| || ||| | ||||||||||| ||||||||||
gtaagcaactatattgaa----------atgttaaaaatattcattcatacaaatgtatt-------tgctaacatattt-ttttcagGACTATAACGCAAAACTCTCTGATTTTGGACTTGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTGTCAACTAGGGTCATGGGAACATATGGATATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA02G02570.1 (Glycine max), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaat-attcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
               | ||  ||||||  ||  | ||   | |||||         | || | ||   ||| | ||  | |   ||||||| |||||||| || ||||| |||||||| || || |||||||| || || ||||||||||| ||||| ||||||||||| |||||||| ||||| ||||
--------------gtaagtgtcaaaaactacaataagattgcattt------ccccctttttatcagtctaatattgtaccgattcagGAGTACAATGCCAAGCTCTCAGATTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA09G37580.1 (Glycine max), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
|||||  |        |  ||  ||    | | |  | | || ||  |   |  |||||    | ||     | ||| |  |||| |||| |||||||| |||||||||||||||||||| || |||||||| ||||| || || || |||||  |||| ||  ||||||||||||| ||||| ||||
gtatgtgagttaaccaggaaa--aaggtttttaattattttttatccatcctccaacataaaaacataaaa-acataattgtttttagGAATACAATGCCAAACTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCAACAAGAGTCATGGGAACATATGGTTATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G16300.1 (Glycine max), 3'ss of exon 5

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
          | ||   | | |  |||  |||||  | | ||| |||   |  |    ||    ||| | |||  |||   | ||||||| |||||||| || ||||| || |||||||| || |||||||| || |||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||
--------gtaagtgccaaattttaaat-tattaccatttttcttttcattccttgatttgatttatatattat-tataactattcagGAATACAATGCTAAGCTCTCAGACTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACTCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA08G40770.1 (Glycine max), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
||| |   |||  | | |   |   | ||| ||     |  |   ||   |||    ||  | |||||  |  || |      ||||||| |||||| | || ||||| ||||||||||| || |||||||| || |||||||||||||| ||||| ||||||||||| |||||||| ||||| ||||
gtaagtggccaaatgttaagttattaccatctttcttttcattccttgatttg----atctttatattattataaca-----attcagGAATACAATTCTAAGCTCTCAGATTTTGGACTTGCAAAAGATGGTCCAGAGGGTGATAAAACCCATGTGTCTACTCGAGTGATGGGAACCTATGGTTATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA19G02360.1 (Glycine max), 3'ss of exon 3

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
||||| |        |   ||| |   | ||||   |   | ||   | |  | || | ||| | |      ||| |    |||  |||| |||||||| || || |||||||||||||| || |||||||| |||||||| || || ||||||||||||||  |||| |||||||| ||||| ||||
gtatgtaggtgaaggtattaattatttcttatt--catcctccaaccaaaaagcaaaaatctaaaa------aaacaaatgtttatagGAATACAATGCCAAGCTTTCTGATTTTGGACTTGCCAAAGATGGTCCTGAGGGGGAGAAGACACATGTATCTACAAGAGTTATGGGAACATATGGTTATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA01G04930.1 (Glycine max), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
    | ||   ||   || | |  ||  | |||  | || | |   |   || |   | ||| ||||| |   |||        ||||||||||||||| || ||||| || ||||| || || |||||||| || || ||||||||||| ||||| |||||||| || |||||||| ||||| || |
----gtaa--gtgcccgaaactacaataagattgcatatttcctcct---ttttgttagtctaatattgccccaat--------tcagGACTACAATGCCAAGCTCTCAGACTTTGGTCTTGCCAAAGATGGTCCAGAAGGTGATAAAACCCATGTGTCTACTCGGGTGATGGGAACCTATGGTTACG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: GLYMA18G49060.1 (Glycine max), 3'ss of exon 4

-gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
 |||||  |        |  ||  ||    | | |  | | |  ||  |   |  |||||    | ||     | ||| |  |||| |||| |||||||| || ||||||||||||||||| || |||||||| ||||| || || || |||||  |||||||  ||||||||||||| ||||| ||| 
ggtatgtgagttaaccaggaaa--aaggtttttaattattttctatccatcctccaacataaaaacataaaa-acataattgtttttaGGAATACAATGCCAAGCTCTCTGATTTTGGACTCGCCAAAGATGGTCCTGAAGGGGAAAAGACACACATATCTACCAGAGTCATGGGAACATATGGTTAT-

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT5G15080.1 (Arabidopsis thaliana), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
            ||  |    ||  | |   |||| |        ||| |||   | ||| |  ||     |||||   |||| ||||||||||||||||||||| || ||||||||||| || |||||||  ||||| |  |  ||||| ||||| |||||| | || ||||| || ||||| ||||
------------gtacgtatctctta-ctctttaggatcaacatcttatatttgcaaattttt-taaccaataaat-cccattgtcagGACTACAATGCAAAACTATCAGATTTTGGACTTGCCAAAGATGCTCCTGATGAAGGCAAAACCCATGTTTCTACTAGGGTTATGGGTACATATGGCTATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: AT3G01300.1 (Arabidopsis thaliana), 3'ss of exon 4

gtatgcaaccatgtttgaga-atcaaaacat----attagaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
|||||    | | ||    | |||||   ||    ||   | ||   | | |   |  |  | |||| |  | |    |     || |||||||| |||||||| ||| | || |||||||| || || |||||||  ||||| |  |  ||||| ||||| ||||||||||||||||| |||||||| || |
gtatgttttcctcttctttatatcaagggatcaacatcttatatacacgtctgtttctttgc-ttctaaagtcttaccatgtcccaatttcagGAGTACAATGCTAAATTATCAGATTTTGGGCTTGCCAAAGATGCTCCTGATGAAGGCAAAACTCATGTGTCTACTCGAGTCATGGGCACTTATGGTTACG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv01s0026g01620.t01 (Vitis vinifera), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatttagattgtaacattctcatatttcttaaat---attcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
               | || |  ||||  | | | ||||   | |||   |  ||| ||  |   || | ||| ||   || |  |||||||| |||||||| ||||| |||||||||||||| ||||||||||| || ||||| ||||| || ||||||||||| || || |||||||||||||||||||
--------------gtaagtaataaaaactgtgataaattcacgtttgtctcctaatatcattccatcttttatatgacatcctatttcagGAGTACAATGCCAAACTTTCTGATTTTGGACTTGCTAAAGATGGTCCCGAGGGAGATAAGACTCATGTATCTACCCGTGTTATGGGAACTTATGGATATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: Vv14s0108g00380.t01 (Vitis vinifera), 3'ss of exon 4

gtatgcaaccatgtttgagaatcaaaacatattagaaatgttcatt-tagattgtaacattctcat----atttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
            ||  | || | ||||    ||  ||||  |  |  ||  || |     ||| ||    |||| | |||  |    || |||||||||||||| || || ||||| |||||||| || ||||| || || || || ||||| ||||||||||||||||| || ||||| || ||||| ||||
------------gtaggtgacttaaaatgctttgcaaatagtagtcctaacttatccttgtcttatttcaatttgtgaaacttgttcttccagGACTACAATGCTAAGCTTTCTGACTTTGGACTTGCCAAAGACGGTCCAGAAGGAGATAAGACACATGTATCTACTCGTGTAATGGGCACCTATGGCTATG

upper sequence: LOC_Os01g40590.1 (Oryza sativa), 3'ss of exon 4
lower sequence: PP1S31_254V6.1 (Physcomitrella patens), 3'ss of exon 4

--------gtatgcaaccatg---tttgagaatcaaaacatattagaaatgttcatttagattgtaacattc-tcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG
        ||| ||||    |   || |      | |   | ||     | |     | |||   | | |   || |    | ||  | ||   | |||||| ||||  || || || ||||||||||| ||||| |||||||| ||||| || || ||||| || ||||| || || |||||||| || ||||| ||||
aatattttgtacgcaatagagactttcgtttcgtatagtctgttccttgtatgggacttgatgtcatcctctgtcctcaaacctagttcttgggtgtcagGATTACACAGCTAAGCTATCTGATTTTGGCCTAGCGAAAGATGGGCCTGAAGGAGACAAAACTCACGTATCAACACGTGTCATGGGCACCTATGGCTATG

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|218487386|gb|FG962477.1|FG962477

EST:     GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCG                         GACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
genomic: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG

EST: gi|58599882|gb|CK010410.1|CK010410

EST:     GGCCAG-TATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCG                         GACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
genomic: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG

EST: gi|38480620|gb|CF964709.1|CF964709

EST:     GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCG                         GACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG
genomic: GGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAG

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), 74 (downstream exon)
Score: 7

AGCACTTGGTGCTGCTAAGGGCCTTGCTTTTCTTCATGAAGAAGCTGAAAGGCCAGTTATCTATCGGGATTTCAAAACTTCAAATATTCTTTTAGACGCGgtatgcaacc ... tcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

agaaatgttcatttagattgtaacattctcatatttcttaaatattcattttcagGACTACAATGCAAAACTCTCTGATTTTGGACTAGCTAAAGATGGCCCTGAGGGTGATAAAACACATGTATCTACTCGAGTCATGGGAACTTATGGATATG