ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TCCTGACCCAGAAGCTAAGGAGCAAGTTGAAATGATACAATGCTCTATATGTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatattttccagtaccttaaatgcgatcatatatgttaggtgctttttgtgttctgattcctgtgtgtttgcctagttgcatcacctgtatctgca...

Basic information

species	Zea mays
transcript	GRMZM2G129431_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G129431_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os06g33810.1 (Oryza sativa), 5'ss of exon 3

TCCTGACCCAGAAGCTAAGGAGCAAGTTGAAATGATACAATGCTCTATATGTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgt-attatattttccagtac-------cttaaatgcgatcatatatgttaggtgctttttgtgttctgattcctgtgtg---tttgcctagttgcatcacctgtatctgca
|||||| ||||||||| |  |||||||||||||||||||||||| ||| |||||||| ||||| || | ||||||||||||||||||||| ||||||||||| | | |   || ||| ||       ||||| ||| ||||||| |||||  | ||  || | |||| || | | ||||   ||||| | | || |  ||||         
TCCTGATCCAGAAGCTGAAAAGCAAGTTGAAATGATACAATGCTGTATTTGTGAGGATTGGTTCCACGAGGATCATATTGGTCTTAACTCCATTGAAGAGgttacttttacttgcagcacgcccttccttaattgc-atcatatttgttaacttctcctttt-ttctaatccttatgtgagttttgcatggctgtacgacct---------

upper sequence: GRMZM2G129431_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA11G01960.1 (Glycine max), 5'ss of exon 4

TCCTGACCCAGAAGCTAAGGAGCAAGTTGAAATGATACAATGCTCTATATGTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatattttccagtaccttaaatgcgatcatat-atgttaggtgctttttgtgttctgattcctgtgtgtttgcctagttgcatcacctgtatctgca
||| || ||||| ||| | || ||||| || |||||||| |||| | ||||||||||||||||||||| ||| ||| |||||||| | |||  ||  ||||| |  ||||||  | |    |   |  | |  | | |   |   |  ||| |||  ||   ||| |||   |  | ||      || |  | | | ||||
TCCAGATCCAGATGCTGAAGAACAAGTAGAGATGATACAGTGCTGTCTATGTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgt-tggtattttggaatttgatgttttagcttctcttaacctttttattttgtgttatcaacttcttgtacttcagtcttcaatgatgagatttttatgca

upper sequence: GRMZM2G129431_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA01G43520.2 (Glycine max), 5'ss of exon 3

TCCTGACCCAGAAGCTAAGGAGCAAGTTGAAATGATACAATGCTCTATATGTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatattttccagtaccttaaatgcgatcatat-atgttaggtgctttttgtgttctgattcctgtgtgtttgcct--agttgcatcacctgtatctgca
|||||| | ||| ||| | || ||||| || |||||||| |||| | ||||||||||||||||||||| ||| ||| |||||||| | |||  ||  ||||| |  ||||||  | |    |   |  | |  | | |   |   |  ||| |||  ||    |  ||||  |  ||||  |||      |  | |||     
TCCTGATCTAGATGCTGAAGAACAAGTAGAGATGATACAGTGCTGTCTATGTGAGGACTGGTTTCATGAGGAGCATCTTGGTCTTGAGTCTTCTGCGGAGgt-tggtattttggaatttgatgtttcggcttctcttaacctttttattttgtgttatcaacattttgtgcttcagccttcagtgatgagatttttattca--

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|22473384|gb|BU037864.1|BU037864

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATA
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATA

EST: gi|87157048|gb|DY401837.1|DY401837

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|31350163|gb|CD434520.1|CD434520

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|28910719|gb|CB331579.1|CB331579

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCA
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCA

EST: gi|31350023|gb|CD434380.1|CD434380

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|71433107|gb|DR814157.1|DR814157

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|71416567|gb|DR803750.1|DR803750

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGGATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|148950203|gb|EC895752.2|EC895752

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|87156860|gb|DY401649.1|DY401649

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAAATGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|148990746|gb|EE032155.2|EE032155

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|148980126|gb|EE026959.2|EE026959

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|71773361|gb|DR971265.1|DR971265

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|94474986|gb|EB703944.1|EB703944

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGC-ACTCTATGAGGA-TTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|149006824|gb|EE040183.2|EE040183

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|71425803|gb|DR806902.1|DR806902

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|71430131|gb|DR811181.1|DR811181

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

EST: gi|91874556|gb|EB404513.1|EB404513

EST:     GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAG                         ATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC
genomic: GTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCAC

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: 130

TCCTGACCCAGAAGCTAAGGAGCAAGTTGAAATGATACAATGCTCTATATGTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatatt ... tctgttgcagATACCAAGAGATGAGGAAGGGGAGCCACTCTATGAGGAATTGATATGCCACAAATGCTCATCTGTCTGCCATTTCTTGAAATTGTATCCAGATACAATTT

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 38

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 44

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 83

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCTGACCCAGAAGCTAAGGAGCAAGTTGAAATGATACAATGCTCTATATGTGAGGACTGGTTTCATGGGGATCATATTGGTCTTAACTCTATTGAAGAGgtattatattttccagtaccttaaatgcgatcatatatgttaggtgctttttgtgttctgattcctgtgtgtttgcctagttgcatcacctgtatctgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA