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

...acttattaagatttcataagaggaatagaagtacatatatagattttctcactacaatgttgtgaggctcacacagatttgtttgctgcttgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG

Basic information

species	Zea mays
transcript	GRMZM2G054706_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G054706_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g04260.1 (Oryza sativa), 3'ss of exon 4

acttattaagatttcataagaggaatagaagtacatatatagattttct-cactacaatgttgtgaggctcacacagatttgtttgctgcttgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG
  | |  | ||  | ||  |     || ||||   | |    ||| | |  | ||  |     |||    |||  | |||  | |  | | || | | |||   ||||||||| ||| || | |||||||||||||| ||||| |||||   ||||||| |  ||||||||||||||||||| || || |||
-ttaaccatgacataatgtggtcgttaaaagtgtgtctgccaattctttataatagcaaaccctgactaacaccaatattactatcatacatgttcttcagGAATCATCATCCGATTCTGTTAGCACAGTGGCAGGAAGGAGTTACACGCTCTGATTTGACCGAAGGGTTCTCTTTTGAGGAATTCATAAAG

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|60341893|gb|DN208866.1|DN208866

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|84976996|gb|DW475418.1|DW475418

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|71436327|gb|DR817377.1|DR817377

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|113704082|gb|EE681586.1|EE681586

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACAGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|32934251|gb|CF039063.1|CF039063

EST:     CCACGCCAGAGCTACCCAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|76931667|gb|DV172796.1|DV172796

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|71326889|gb|DR800102.1|DR800102

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|87153522|gb|DY398311.1|DY398311

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACAGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|76923534|gb|DV169534.1|DV169534

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|149044688|gb|EE047661.2|EE047661

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|211234326|gb|FL299527.1|FL299527

EST:     CCACGCCAGAGCTACACAATGAAAACGGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACAGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|71428268|gb|DR809318.1|DR809318

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|149044689|gb|EE047662.2|EE047662

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCCATTTTGCT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCT

EST: gi|76017108|gb|DT944278.1|DT944278

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|76283964|gb|DV023532.1|DV023532

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTT

EST: gi|9731636|gb|BE510388.1|BE510388

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACAGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|37379721|gb|CF626613.1|CF626613

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACAGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|211462811|gb|FL454173.1|FL454173

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACAGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|211234325|gb|FL299526.1|FL299526

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGNGGCAGGACGGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

EST: gi|21331905|gb|BQ487286.1|BQ487286

EST:     CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAG                         ACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACAGAGTAACACGTGT
genomic: CCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGT

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: 46 (upstream exon), 48 (downstream exon)
Score: 89

CCCTTTTAACCTCTTCAACCGAAACAGATTCAGACTTGAATCTACTGCGTCCACGCCAGAGCTACACAATGAAAACAGGGCGTACATTAGATGATGTCAGgtagatgttt ... tgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG

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

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 94

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 82

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttctcactacaatgttgtgaggctcacacagatttgtttgctgcttgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG

                               atttgttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttattaagatttcataagaggaatagaagtacatatatagattttctcactacaatgttgtgaggctcacacagatttgtttgctgcttgctgtgcagACTTCATCATCCAATTTTGCTGGCACAGTGGCAGGACGGAGTAACACGTGTTGATTTGGCTAAAGGGTTCTCTTTTGAGGAGTTTATGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - gaatagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - atgttgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcacaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgctgc