ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...aatcatgaatgggtgtttgatcttctgacaggtatctatctgaatttttttaaattaggatggtcatttccaactctacccctgctttgctgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

Basic information

species	Zea mays
transcript	GRMZM2G158237_T05
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158237_T05 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os09g36670.1 (Oryza sativa), 3'ss of exon 5

-------------------------------------------------------------------------aatcatgaatgggtgtttgatcttctgacaggtatctatctgaatttttttaaattaggatggtc-atttccaact-ctacccctgctttgctgtctt---gcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG
                                                                         | |     ||   | |   ||     ||    ||  | | |  || || || |       ||  |   |||  | |    | | || | ||||||| |   ||||| ||| |||| ||||| |||||||||| |||||| |||||||| ||||||||||| || || ||||||||||||||
gtcagaaattcagaatgctcaattgatttgtactttctactttacctttatttatgagttatatgtatcgctaagttgcacatttttctcctatacatgga-gcatagatttttagatattctttatgcgctctgccctgcttctgattatctctcttggtctgctgtcatcatgcagGTGTTATTGCCATGGCAAATTCTGGACCTGATTCCAATGGATCGCAGTTTTACATTACCACAATCAAGACAAGCTG

upper sequence: GRMZM2G158237_T05 (Zea mays), 3'ss of exon 4
lower sequence: Vv03s0038g02200.t01 (Vitis vinifera), 3'ss of exon 5

-------------------------------------------aatcatgaatgggtgtttga-----tcttctgacaggtatctatctgaatt------tttttaaattaggatggtcatttccaactctacccctgct-----------ttgctgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG
                                             || || ||      | ||     |||  | | | || |  ||  | |||      |||  | |||  | | ||   || |  |  | | | |  |           |||||   ||| ||| |||||| | |||| |||||| |||| |||||||||||| |||||||||| ||| || ||  ||||| | |||||
gttctctattacatctctttatttggttgattttttcttctggtttcttgtatactccctagacaaattctctttaaaagttttcatagggattcaaaattttcaagattgagtttgttcctttctcccttcctctttgtgaaaccatatattgcttggttgtagGTGTTGTTTCCATGGTGAATTCAGGACCTGATTCTAATGGCTCTCAGTTTTTCATCACCACAGTCAAGGCTAGCTG

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|76926335|gb|DV170814.1|DV170814

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTTTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|87155387|gb|DY400176.1|DY400176

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|71434184|gb|DR815234.1|DR815234

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGTTATGGGGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|30704816|gb|CD058610.1|CD058610

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|213175357|gb|FM185315.1|FM185315

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|76922694|gb|DV169125.1|DV169125

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|78024054|gb|DV492441.1|DV492441

EST:     CCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGATATGGCGAATTCTGGACTTGATTTTAATGGATTTCAGTTTT
genomic: CCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|76926341|gb|DV170815.1|DV170815

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|60346388|gb|DN213361.1|DN213361

EST:     TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

EST: gi|211328997|gb|FL454093.1|FL454093

EST:     GGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAG                         GGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT
genomic: TGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTT

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: 43 (upstream exon), 49 (downstream exon)
Score: 114

CAGGGCGGTGACATAGTTAGAGGCGACGGTAAAGGGAGTGAGTCTATATATGGAGGCATCTTCCCAGATGAGAATTTCACTGTAAAACATACACATCCAGgtgtgattgt ... tgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 121

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 89

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 100

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttttaaattaggatggtcatttccaactctacccctgctttgctgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

                                       ctttgct  CT-rich tract
     taaatta  TA-rich tract

Putative cis-regulatory sequences

atgc	intron	ATGC	exonic elements by Pertea et al.
ATGC	exon	atgc	putative intronic elements
		ATGC	putative exonic elements identified for retained introns

        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aatcatgaatgggtgtttgatcttctgacaggtatctatctgaatttttttaaattaggatggtcatttccaactctacccctgctttgctgtcttgcagGGGTTGTTGCTATGGCGAATTCTGGACTTGATTCTAATGGATCTCAGTTTTACATAACTACTATCAAGACAAGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG