ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACTTGTTGCTGCTAGGATTGAAGCTGAAGAGAGACTAAACAACCAGCGATTGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaagttatatgggcagtgtgcatcactgattttattacatagtagtagaaagtacacatgtttatgtataaaatggatgcatgcggggttggtc...

Basic information

species	Zea mays
transcript	GRMZM2G343688_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G343688_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g37630.1 (Oryza sativa), 5'ss of exon 2

ACTTGTTGCTGCTAGGATTGAAGCTGAAGAGAGACTAAACAACCAGCGATTGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaagttatatgggcagtgtgcatcactg-att-ttattacatagtagta-gaaagtacacatgtttatgtataaaatggatgcat--gcggggttggtc
||| ||||||||||||||||| ||||||||||| |||||||| || || |||||||||||||||||||||||||| |||||||||||||||||||||||||||   |||  | |   |||  | |   |   |  ||| ||  | |    |||||  | ||||  |||| |   || ||| |||| | ||      ||||  |  
ACTCGTTGCTGCTAGGATTGATGCTGAAGAGAGGCTAAACAATCAACGCTTGCGTGAGGAACAAGATGCTGCTTATAGAGCTGCACTTGAAGCTGATCAGgtatgctaaactctggaggccatttctgttcttatattattgatgcgctttagtacaagagtatgcatgct---gtgtaatatgggttcaacgatagggtctg--

upper sequence: GRMZM2G343688_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA20G35940.1 (Glycine max), 5'ss of exon 2

ACTTGTTGCTGCTAGGATTGAAGCTGAAGAGAGACTAAACAACCAGCGATTGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaa----cttaagttatatgggcagtgtgcatcactgattttattacatagtagtagaaagtacaca---tgtttatgtataaaatggatgcatgcggggttggtc----------------------------------------------------------------
 |||| ||| |||||| |||| || ||||| |||  ||| ||   ||| ||  | ||||| ||||||||||| ||||| |||||||||||||||||||| |||      ||    | |||||    | ||| |   |  | | |||   | || ||    | | ||     | ||| | |  ||  |  |        |    || |                                                                
CCTTGCTGCGGCTAGGCTTGATGCAGAAGAAAGAAGAAATAATATGCGCTTAAGGGAGGAGCAAGATGCTGCATACAGGGCTGCACTTGAAGCTGATCAAgtatgctttttgtagtgtatggttgttctgcttgtttcttatcatt-ttttgtggtctctactccatggcttttttttttccaatctcaacatcccttgcagaggcctttatttagaaagaactgacctgttactgttagtgtggattaatgttgttgtatgtgtgtccag

upper sequence: GRMZM2G343688_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA10G31660.1 (Glycine max), 5'ss of exon 2

ACTTGTTGCTGCTAGGATTGAAGCTGAAGAGAGACTAAACAACCAGCGATTGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaa----cttaagttatatgggcagtgtgc--atcactgattttattacatagt----agtagaaagtaca-catgtttatgtataaaatggatgcatgcggggttggtc--------------------------------------------------------------
 |||||||| |||||| |||| || ||||| |||  ||| ||   ||| ||  | ||||| ||||||||||| ||||| |||||||||||||||||||| |||      ||    | |||||  | | |||   |  |  ||  | ||   | ||    | |  |  |     | | |||   |||   |      | ||| | |    |                                                               
TCTTGTTGCGGCTAGGCTTGATGCAGAAGAAAGAAGAAATAATATGCGCTTAAGGGAGGAGCAAGATGCTGCATACAGGGCTGCACTTGAAGCTGATCAAgtatgctttttgtagtgtatggttattctgcttgtttcctatcattttttgtggtctctactccatggcttgtccttttttcctatctcaacatcccttgcagaggcctttattcagaaagaactggcctgttactgttgctgtggattaatgttgtacgtatgcatgtccag

upper sequence: GRMZM2G343688_T02 (Zea mays), 5'ss of exon 2
lower sequence: AT4G10790.1 (Arabidopsis thaliana), 5'ss of exon 2

ACTTGTTGCTGCTAGGATTGAAGCTGAAGAGAGACTAAACAACCAGCGATTGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaagttatatgggcagtgtgcatcactgattttattacatagtagtagaaagtacacatgtttatgtataaaatggatgcatgcggggttggtc--
  | ||  |||||||| |||| || || || |||  || ||| | |||  || | ||||||||||||||||||||| | ||||| |||||||| ||||| |||  ||   || | |     ||  || |        ||   |     |  |    |||  || ||| ||  | |     |      ||    | || |   
TTTGGTAACTGCTAGGGTTGAGGCGGAGGAAAGAAGAACCAATCTGCGTCTGAGAGAGGAACAAGATGCTGCTTACCGTGCTGCTCTTGAAGCCGATCAAgtatgtt---ttctgttctttgtaggcctgttcagaattgacaagactttatgattagtctac-tgtctaaatttgtggcgt-catttgttctgctgattag

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|211061442|gb|FL105773.1|FL105773

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|9953320|gb|BE639903.1|BE639903

EST:     CTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGGAAAGACGTGAAAGAGAGGCT
genomic: CTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|78083899|gb|DV512292.1|DV512292

EST:     AAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTTGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: AAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|211470731|gb|FL464832.1|FL464832

EST:     GCGTGAGG-ACAAAGATGCTGCTTACAGAGCTGCACTTGCAGCTGATCAG                         GCCAGGG-ACGTGAAAGGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGC
genomic: GCGTGAGGAAC-AAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAA-GGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGC

EST: gi|76288092|gb|DV027660.1|DV027660

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|89246999|gb|DY618785.1|DY618785

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|148946845|gb|EC892122.2|EC892122

EST:     AAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGAAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: AAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|9732547|gb|BE511299.1|BE511299

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGGAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|148958551|gb|EC904794.2|EC904794

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|78111230|gb|DV529627.1|DV529627

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|9952944|gb|BE639527.1|BE639527

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGGAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|211329018|gb|FL455397.1|FL455397

EST:     CAGAGCTGCACTTGAAGCTGATCAG                         GCCAGAGAACGTGAAAGGTTAGAGGAGCTGAAAAGACGTGAAAGAGAGACT
genomic: CAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|23357488|gb|BU645137.1|BU645137

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGGAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|9461590|gb|BE453807.1|BE453807

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGGAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|149075103|gb|EE163593.2|EE163593

EST:     ACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: ACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|211329017|gb|FL455396.1|FL455396

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|14245022|gb|BG842960.2|BG842960

EST:     GCTGCACTTGAAGCTGAACAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: GCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|32840228|gb|CD979909.1|CD979909

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTTGAAAGGTTAG
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGT-GAAAGGTTAG

EST: gi|149104942|gb|EE290413.2|EE290413

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|211061441|gb|FL105772.1|FL105772

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGGAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

EST: gi|14203011|gb|BG836688.1|BG836688

EST:     TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAG                         GCCAGGGAACGTGAAAGGTTAGAGGAACTGGAAAGACGTGAAAGAGAGGCT
genomic: TGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCT

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), 48 (downstream exon)
Score: 149

ACTTGTTGCTGCTAGGATTGAAGCTGAAGAGAGACTAAACAACCAGCGATTGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaag ... atattaccagGCCAGGGAACGTGAAAGGTTAGAGGAACTGAAAAGACGTGAAAGAGAGGCTGCAGAGGCTGAGAAAAAGCGTAAAGAAGAGGAGGAAGCTGTAGCAAGGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 220

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 187

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTTGTTGCTGCTAGGATTGAAGCTGAAGAGAGACTAAACAACCAGCGATTGCGTGAGGAACAAGATGCTGCTTACAGAGCTGCACTTGAAGCTGATCAGgtaacttaagttatatgggcagtgtgcatcactgattttattacatagtagtagaaagtacacatgtttatgtataaaatggatgcatgcggggttggtc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT