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

...agaattaagatgtggtattctgcatacaagtcttctcctgtctttatgaagctgatgtgttgtgtttaggcatgtatctaacaataattccttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTTACGTTAGCATCGGGTACCCCTTTGGTCTGATGGCCTCAGTCCTATTCGG

Basic information

species	Zea mays
transcript	GRMZM2G024211_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G024211_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os02g48590.1 (Oryza sativa), 3'ss of exon 1

agaattaagatgtggtattctgcatacaagtcttctcctgtc-tttatgaagctgatgtgttgtgtttaggcatgtatctaacaataattccttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTTACGTTAGCATCGGGTACCCCTTTGGTCTGATGGCCTCAGTCCTATTCGG
|  || | ||  |  |||||  ||||||||| |||| |   | ||  || ||||| |   |  || |||| ||| ||||||     | || | ||||||||| |||||||| || ||||||||||||||||| || ||  | || |||||||| |||||||| |||||||| |||||||| |||||||| |||||||| ||
aagataatgac-tcatattccacatacaagttttcttcaaccattcttgcagctgttagatcatgcttagtcatatatctatatccactttcctgatgcagGAGCACCAATAGCGGGATCTGCAGTTGATAAGGTTGACCAGGTCATTGGTTATGTTAGCATTGGGTACCCATTTGGTCTAATGGCCTCGGTCCTATTTGG

upper sequence: GRMZM2G024211_T01 (Zea mays), 3'ss of exon 1
lower sequence: PP1S97_81V6.1 (Physcomitrella patens), 3'ss of exon 2

agaattaagatgtggtattctgcatacaagtcttctcctgtctttatgaagctga---tgtgttgtgtttaggcatgtatctaacaataattccttga--tgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTTACGTTAGCATCGGGTACCCCTTTGGTCTGATGGCCTCAGTCCTATTCGG
    |||     |  | || |  | |  |  ||  | | |  ||| |||| ||||    | |||    ||   |      || ||  |  |  | |||  |||||||||||| ||||| ||||||||| ||||| ||||| | || ||  | || |||||     | || || || |||||  || | ||||| ||||| |||||
----ttatttatttattttttttacatcaacctgttgcagatttt-tgaaactgaaaacgggttaaagttttcctgaagccttacttttgtgtcgtgaaatgcagGGGCACCCATTGCAGGATCTGCAATTGATGAAGTGAAGGAGGTTGTAGGCTACGTAGCTTTGGGTTATCCTTTTGGAATGTTAGCCTCCGTCCTGTTCGG

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|211540885|gb|FL340418.1|FL340418

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|60342385|gb|DN209358.1|DN209358

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211258266|gb|FL355090.1|FL355090

EST:     CGCAGAGAACATCAAGGCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211472959|gb|FL343113.1|FL343113

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|148964652|gb|EC905936.2|EC905936

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211020747|gb|FL319293.1|FL319293

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211224416|gb|FL320295.1|FL320295

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211306570|gb|FL359156.1|FL359156

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGT

EST: gi|211090659|gb|FL308854.1|FL308854

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211008014|gb|FL361157.1|FL361157

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|94476128|gb|EB705086.1|EB705086

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211015163|gb|FL318463.1|FL318463

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211377472|gb|FL308237.1|FL308237

EST:     CGCAGAGAACATCAAGCCGCGCG-CATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211500943|gb|FL349211.1|FL349211

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211374882|gb|FL313293.1|FL313293

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCAC-AATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211375800|gb|FL346981.1|FL346981

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGA
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGA

EST: gi|94476127|gb|EB705085.1|EB705085

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|211118163|gb|FL349422.1|FL349422

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

EST: gi|14529472|gb|BI096605.1|BI096605

EST:     CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTG                         GGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGGT
genomic: CGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTT

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), 43 (downstream exon)
Score: 43

CTCACGGGCTCCACCGAAGTCGGGGACGTCGTCGCCGTCTGCCGATGGGTCGCAGAGAACATCAAGCCGCGCGGCATCCTCCTCGTCGGATCCTCAGCTGgtagactcca ... cttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTTACGTTAGCATCGGGTACCCCTTTGGTCTGATGGCCTCAGTCCTATTCGG

Block sizes: 48 (upstream exon), 42 (downstream exon)
Score: 57

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 27

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 53

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atgaagctgatgtgttgtgtttaggcatgtatctaacaataattccttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTTACGTTAGCATCGGGTACCCCTTTGGTCTGATGGCCTCAGTCCTATTCGG

                                          ttcctt  CT-rich tract
                             tatctaacaataatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaattaagatgtggtattctgcatacaagtcttctcctgtctttatgaagctgatgtgttgtgtttaggcatgtatctaacaataattccttgatgcagGGGCACCAATTGCCGGATCTGCAGTTGATAAAGTGGATGAAGTGATTGGTTACGTTAGCATCGGGTACCCCTTTGGTCTGATGGCCTCAGTCCTATTCGG

- - - - - - - - - - tgcatac
- - - - - - - - - - - - - - - - -tctcctg
- - - - - - - - - - - - - - - - - - - - - - - - - gctgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtgttt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aacaata