ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

Basic information

species	Zea mays
transcript	GRMZM5G824405_T02
intron #	11
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA11G27410.1 (Glycine max), 3'ss of exon 19

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
                             ||  |   |  |  |||   |   ||  | |    ||  || ||||  |     || |       ||||| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | 
----------------------------gtactttttatgatttttcaagctgagctttttccttaaata-atgttgattccatgca------ccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G37520.3 (Glycine max), 3'ss of exon 13

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaacctttt--cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
                            |  | | | | |  | |   | |  |   |    | | | | ||  |||   | ||||   | | |  ||||| |||||  | || |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | 
---------------------------gtacttttaaattttaatggctattcaaggtgagcttttgctttaaataa---tgttgatttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 21

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaacctttt--cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG-----
                            |  | | | | |  | |   | |  |   |    | | | | ||  |||   | ||||   | | |  ||||| |||||  | || |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || |      
---------------------------gtacttttaaattttaatggctattcaaggtgagcttttgctttaaataa---tgttgatttcatataccagGTTTATGAGACCGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAAGTAAG

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA02G39390.1 (Glycine max), 3'ss of exon 13

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaacctttt--cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
            ||| |  | | | || |  | ||| | |  | |   | |  |   |    | | | | ||  |||   | ||||   | | |  ||||| |||||  |||| |||||||| |||||||||||||||||||||||||  |||||  | || || ||| || | 
-----------gcaagtc-tttcatatgtactttcaaattttaatggctattcaaggtgagcttttgctttaaataa---tgttgatttcatatgccagGTTTATGAGACGGTAGAAGAAGGATCTTACATAAAAATGATTGACATGGCCAGTGGACATGGAGGGCAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA18G06770.1 (Glycine max), 3'ss of exon 15

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatag-tatagttatatgtaaacattttgaaaccttt---tcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
                           | ||||| ||  |  | ||||| | |      ||| ||   || |   |||| | | |  |  || |    ||||| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | 
------------------------gcaagtatat-accgtgtactttttatgattgtgctagctacctttttccttaaataatgttgattctatgcaccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: GLYMA11G27870.1 (Glycine max), 3'ss of exon 14

gtctgtaattgccaaattatattaaatattatatcacaatacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
          || |   ||||     || | | | |  ||    ||   |   ||  | |    ||  || ||||  |     || |       ||||| |||||  | ||  | ||||| |||||||||||||||||||| ||||| |||||| | || || ||| || | 
----------gcaagtctataacgtgtacttt-ttatgatt--gttcaagctgagctttttccttaaata-atgttgattccatgca------ccagGTTTATGAGACAGTTAATGAAGGATCTTACATAAAAATGATTGATATGGTCAGTGGGCATGGTGGACAAATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: AT1G07110.1 (Arabidopsis thaliana), 3'ss of exon 13

------------gtctgtaattgccaaat-tatattaaata----ttatatcacaatacattttttgtcaag--aatatagtatagttatatgtaa-acattttgaa---acctttt--------cagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
              ||| | || | |||  | |  ||| ||    ||| | |  | |  | ||||  |  |   |  || || | | ||  |   | | || ||||    ||  |||        ||||| ||||| || || ||||||||||| ||||| ||||||||||| ||||| |||||||| || || ||  || | 
gtcggtacacaaacctgcactttctaaacgtgtcctaattactttttaaagcttagttaacttttctttgatgcaccatcgtcttggtacttaagacaaatgttgagcttactctttttttttgccagGTTTATGAGCCTGTAGAAGAAGGTTCGTACATCAAAATGATTGATATGGTCAGTGGGAACGGTGGACAGATACAA

upper sequence: GRMZM5G824405_T02 (Zea mays), 3'ss of exon 11
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 13

---gtctgtaattgccaaattatattaaatattatatcaca-atacattttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttt-tcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG
   || |      ||  | ||||  | | |  ||   | || ||   | |||||| ||  || |        |  |  |||||| ||     ||| |  ||||| ||||| || ||||||||||| |||||||| ||||||||||| |||||| ||||  | |  || ||  || ||
gtagtttcctggagcttacttatgatgattggtactactcatatttgtattttgtgaaagattt-------ctgaaaataaacaattgtgctcctgtaccagGTTTATGAGCCAGTGGAAGAAGGCTCTTACATCAAAATGATTGATATGGTTGGTGGCCAAGATGGACAGATACAG

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|84980594|gb|DW530943.1|DW530943

EST:     TGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGGAC-TATTATGAAAAG                         GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
genomic: TGAAGCTGGTGTACAAGATTTCAAAGAGCGATTG-ACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT

EST: gi|211189269|gb|FL030572.1|FL030572

EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGGCCTATTATGAAAAG                         GTCTATGCAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGT
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATG-AACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGT

EST: gi|19437252|gb|BM953662.1|BM953662

EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAG                         GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTG
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTG

EST: gi|5895775|gb|AW037021.1|AW037021

EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAG                         GTCTATGAACCGGNGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT

EST: gi|67010650|gb|CO439399.1|CO439399

EST:     TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGGCCTATTATGAAAAG                         GTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT
genomic: TTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTT

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 4 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 100

AACAGATTTTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 171

AACAGATTTTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 189

AACAGATTTTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 416

AACAGATTTTGAAGCTGGTGTACAAGATTTCAAAGAGCGATTGACCTATTATGAAAAGgtctgtaatt ... accttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attttttgtcaagaatatagtatagttatatgtaaacattttgaaaccttttcagGTCTATGAACCGGTGGAAGAAGGTTCTTACATAAAAATGATTGACATGGTTAGTGGGAAGGGGGGCCAACTAAAG

                                              ccttttc  CT-rich tract
             aatatagtatagttat  TA-rich tract

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

RNA-Seq data