ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtacatccgatatcctgtatatgagttcgtggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT

Basic information

species	Zea mays
transcript	GRMZM2G006977_T01
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 5

gtacatccgatatcctgtatatgagttcgtggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
                                 |   | |   | || || |   |   |||  ||||    |  | |||| |||||||| | ||    | | |||||    |  | ||| |||   ||||||||||||||||||| |||||||| ||| |||||||||| |||||||||||||| ||||| || || ||||||||||| || ||||| |||||| |||||||
----------------------------taaactaacataaaatttattaatgtggaaaatcaagaat---ttcctagtttgtttcataact-tactcttgactgttctttgtacttctgcttggc-attcagGGAGTGCTCCTCTTACTGCTGTCCAACTGCTCTGGGTTAACATGATCATGGACACACTAGGAGCACTGGCATTGGCAACTGAACCTCCAAACGATGAACT

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5

gtacatccgatatcctgtatatgagttcgt-ggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
                            || ||||| | ||   |  || | || |  || ||   ||    | |||||  |   |      | | || | ||      ||  | ||| | ||      |||||| ||||||||| | |||||||| |||||| | ||||| |||||||||||||| ||||| || || || || || || ||||| || |||||| | || ||
----------------------------gtaggtttagtaagaat--accaattcaatgtctcgaaaagaatcattttggattcct------tgtttgacaca------gctcttatgataatc-----ttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G22950.1 (Arabidopsis thaliana), 3'ss of exon 5

gtacatccgatatcctgtatatgagttcgtggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatat-gtctcattgttcgcattcatgctgattgctgatt-------cagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
                            ||   ||  | |      | ||  |||   | |  | | |  | ||||  ||| ||| | || ||||| ||||   | |     || |   |  || || | |       |||| ||||||||||| |||||||| ||| |||| ||||| |||||||||||||| ||||| || || || ||  | || |||||||| || ||||| || ||
----------------------------gtaagttaaagaa-----attagctgattctgtttttattcaaattttcattt-ttttacaattatattgtcttcgtttctatctttacttttgtttctaaattaattcacagGAAGTGCTCCTCTAACTGCTGTTCAACTGCTTTGGGTTAACATGATCATGGACACACTTGGAGCTCTTGCTCTAGCTACAGAACCTCCGAACAACGAGCT

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 4

gtacatccgatatcctgtatatgagttcgtggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
     |  ||   ||      ||  |      |||  || |    |||| | |     | ||   |||  |||| || ||| ||      | || | | | |||  |    ||  |    |   ||   | ||| | |||||| ||||| ||||| ||  | || ||||||||||||||||||||||||||||| || || ||||| || || || || || |   ||||  |
----gtaagaagaccccatcttgcttcttccatttcaaagt----tacttccttgttttgtc--aaataaacttcttcttttttctccctacattttttttattcctttttttttt--caaacact---taagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACCGAGCCACCTACTGATGACTT

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv18s0001g09150.t01 (Vitis vinifera), 3'ss of exon 5

gtacatccgatatcctgtatatgagttcgtggtttggaaatcctctactacttgagcgt-atcctgaatgtactttttgtttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
                ||||||     |     ||||   |   | | |   |     | ||  ||||| |   |||||  | ||    |  |  |    |  || || |  || |||     ||  |  ||||| | |||||| || || || || ||  | || |||||||||||||| |||||||||||||| || || ||| |||| || ||||| || ||  ||||  |
----------------gtatatagaccctgatgttggctcttgcccattctgtatttatcattttgaatttctgttttgcatgttattcatcttcac-ctttgttttttgggttgatg-----tgtggtctcagGAAATGCTCCCCTGACCGCGGTTCAGCTTCTGTGGGTCAACATGATTATGGATACACTGGGAGCACTTGCACTGGCTACTGAACCTCCTAATGATGAGTT

upper sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 5

gtacatccgatatcctgtatatgagttcgtggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
     |  ||   ||      ||  |      |||  || |    |||| | |     | ||   |||  |||| || ||| ||      | || | | | |||  |    ||  |    |   ||   ||||| | |||||| ||||| ||||| ||  | || ||||||||||||||||||||||||||||| || || ||||| || || || || || |   ||||  |
----gtaagaagaccccatcttgcttcttccatttcaaagt----tacttccttgttttgtc--aaataaacttcttcttttttctccctacattttttttattcctttttttttt--caaacact---tcagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACTGAGCCACCTACTGATGACTT

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|32923200|gb|CF028012.1|CF028012

EST:     TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAG                         GGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG
genomic: TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAGgtacatccga ... gctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG

EST: gi|33099646|gb|CF059606.1|CF059606

EST:     TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAG                         GGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG
genomic: TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAGgtacatccga ... gctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG

EST: gi|32923223|gb|CF028035.1|CF028035

EST:     TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAG                         GGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG
genomic: TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAGgtacatccga ... gctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG

EST: gi|32922458|gb|CF027270.1|CF027270

EST:     TGTCAATGCGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAG                         GGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG
genomic: TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAGgtacatccga ... gctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG

EST: gi|33099616|gb|CF059576.1|CF059576

EST:     TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAG                         GGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG
genomic: TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAGgtacatccga ... gctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG

EST: gi|32941460|gb|CF046279.1|CF046279

EST:     TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAG                         GGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG
genomic: TGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAGgtacatccga ... gctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGG

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: 96

GGTCGATCAGTTTACATCAACATTCAGAAGTTTGTGCAGTTTCAGCTCACTGTCAATGTGGTTGCTCTGGTGGTAAACTTCTCCTCAGCTTGCCTGACAGgtacatccga ... gctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 123

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 50

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT