ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

...actatgggttatagtcatttttcttattctctatactgtaccgccatgcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG

Basic information

species	Zea mays
transcript	GRMZM2G376731_T01
intron #	13
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os04g59494.2 (Oryza sativa), 3'ss of exon 13

----------------------------------------------------------------actatgggtt-atagtcattttt--cttattctctatactgtaccgccatgcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG
                                                                  | ||  || | | ||| ||||   || |||      || | | ||    | |||   | |  ||  ||||| | |  ||| || |  | ||| |  ||||||||||||| || || || ||||||||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||||||||| |||
gtatttttatcaattaactattgctgtatttaattccttgaacttcattaggaaaagagtagcatgtgtgtattgagactcacttttgatttcttcatctgtctattctgcttcccttctcattgtgaat--tgtacctatcctaacatgttct-attcatttgcagATTGTTGCTTTTCTTATTCCACTTCTTGACGATAAATTTCCTCTTATACGGAGTATTACTTGTTGGACCCTCTCCCGATATAGTAAATTCATTGTACAG

upper sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA10G42960.1 (Glycine max), 3'ss of exon 13

--actatgggttatagtcatttttcttattctctatactgtaccgccat-gcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG
      |   |||  |    |  | ||||  ||||   | |   ||| | || |||| ||    || | | | |||  | ||   ||  | ||  |  |  ||||||| || || ||  |||| |||||||||||||| |||||||| ||||| |||||| | || ||||| || || |||| ||||||||| ||| |||||
cattcttattttactgagtctggttttatgatctactttatgtggcccttgcttcttactg---attcagaatattaaacaattgattgttatgcatttatagATTGTGGCATTTCTTGTCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTATTCAG

upper sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA20G24040.1 (Glycine max), 3'ss of exon 13

--actatgggttatagtcatttttcttattctctatactgtaccgccat-gcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG
      |   |||  |    |  | || |  |||| | | |   ||| | || |||| |||   || | | | |||  | ||   ||  |  |  |  |  ||||||| || || || ||||| |||||||||||||| |||||||| ||||| |||||| | || ||||| || || |||| ||||||||| |||||||||
cattcttattttactgagtctggttttgtgatctacattatgtggcccttgcttcttacta---attcagaatattaaacaattcattgttttgcatttatagATTGTGGCATTTCTTATCCCTCTTCTTGATGATAAGTTTCCTCTGATACGAAGTATTTCATGCTGGACACTATCACGATTTAGCAAATTTATTGTTCAG

upper sequence: GRMZM2G376731_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv18s0001g00910.t01 (Vitis vinifera), 3'ss of exon 13

actatgggttatagtcatttttcttat-tctctatactgtaccgccatgcgtcttgctatatatgctgtacattttataagatatcttcattg--aaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG
  |     || |  |  || |||   | |||   | || ||      | |   |  || ||| |  |||    ||  |  || | ||  |||   | ||||||||||| || || || ||||| ||| | || |||||||||||| | ||||| |||||||| || ||||| || ||||| | |||||||||||||||||||
-attcatcttgttctagttcttcaggtatctggttgctctaatatttt-caagtaactgtat-taatgtcaggttattgtgacaactcaattcttacatgcagATTGTGGCTTTTCTCATCCCCCTTTTAGACGATAAATTTCCTTTGATACGAAGTATTACTTGCTGGACCCTTTCTCGGTTTAGCAAATTCATTGTTCAG

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: 47 (upstream exon), 48 (downstream exon)
Score: 152

AACAGATGACAATTCTTGGAAGGAGAGGGAAACTGCTGTTTTGTGTCTAGGCGCTATAGCAGAGGGGTGCATTGGTGGTCTATACCCACACCTTCCTCAGgtaatcttaa ... tgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 154

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 136

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG

                                      tcttcatt  CT-rich tract
                         attttataagatatct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
actatgggttatagtcatttttcttattctctatactgtaccgccatgcgtcttgctatatatgctgtacattttataagatatcttcattgaaatgcagATTGTTGCCTTCCTAATCCCACTTCTTGATGATAAATTTCCTCTTATACGGAGTATTACGTGTTGGACGCTCTCTCGATATAGCAAATTCATTGTTCAG

- - - - - - - - - - - - - - - - - -ctgtacc
- - - - - - - - - - - - - - - - - - - - - gccatgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tatgctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tacattt

Data associated with selected splice site

Sequence

Basic information

Orthologous splice sites

RNA-Seq data

Putative cis-regulatory sequences