ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

gtacggaattaccaatgcttataattgtaaataaaatgtctgaatttaatagtagggcgtgtttggataagtcttccattggtaactctgacttctgatatggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG

Basic information

species	Zea mays
transcript	GRMZM2G112609_T01
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g63520.1 (Oryza sativa), 3'ss of exon 3

-----------------------------------------gtacggaattaccaatgctt----ataattgtaaataaaatgtctgaatttaatagtagggcgtgtttggataagtcttccattggtaactctga------cttctgatatggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG
                                          |||   ||    |  | |     | || | | |   |  |    |  | | | | |||    |  |||| |   |  |     | | | | | |      | |||  |||||    |||||||||||| |||||||||||||| || || || |||||||||||  ||||  |||| |||||||| ||||| || ||||| |||
gtacgagattagtacaagcattatacttggtttttggttttctacaccatcgttaggggtgcaggacaaatcttagggattttctgggctctgaaaatag--tcttcttgggtgcatacttagaagttgagttttagtaattcctctcgtatggacctgcagGTTTATGTATGGAGCAAGCACAATCCCTTCATTCATATGAGCTTCTTGGGTTTGTTCACCTTTACTGCTGCTTATTTACCTTGG

upper sequence: GRMZM2G112609_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv10s0116g00010.t01 (Vitis vinifera), 3'ss of exon 1

gtacggaattaccaatgcttataattgtaaataaaatgtctgaatttaatagtagggcgtgtttggataa-gtcttccat---tggtaactctgacttctgatatggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG
      | |||    | ||| |  |   | ||| ||  | |    ||  |   ||    |||      |  || ||  ||   | || ||||||  || |  | | | |   ||||||||||| ||||||||||| || ||||||||||||||||| ||  ||||||| |||||||| || || || ||| | ||||||
---gttagttaatttttctt-tgctcacacatagaagatgttttattggttacagtcattgtgcaacaactgttttggatgtcttgttactctg-tttttcctgttgta---cagGTTTATGTGTGGAGCAAGCAAAATCCTTTTATCCATATGAGTTTCTTGGGCCTCTTTACCTTCACAGCGGCCTACCTTCCATGG

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|6601841|gb|AW256282.1|AW256282

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|76917920|gb|DV167073.1|DV167073

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|91048268|gb|EB158686.1|EB158686

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|211076091|gb|FL368274.1|FL368274

EST:     GACATTTGCCAGAATTCTGTTCTTGAMGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: GACATTTGCCAGAATTCTGTTCTTGA-GCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|32919420|gb|CF024232.1|CF024232

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTC

EST: gi|50333879|gb|CO529005.1|CO529005

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|211475590|gb|FL117469.1|FL117469

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTT
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTT

EST: gi|56382233|gb|CV984902.1|CV984902

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|76012317|gb|DT939487.1|DT939487

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|91878613|gb|EB408570.1|EB408570

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|148970116|gb|EE021054.2|EE021054

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

EST: gi|60342635|gb|DN209608.1|DN209608

EST:     AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATG                         GTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC
genomic: AGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGC

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: 87

TGTCCTAACTGGCATTGTTCTGATCGGAGGGATGATACCTTACATTTCTGAGACATTTGCCAGAATTCTGTTCTTGAGCAATTCATTGACATTTATGATGgtacggaatt ... ggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 110

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 166

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacggaattaccaatgcttataattgtaaataaaatgtctgaatttaatagtagggcgtgtttggataagtcttccattggtaactctgacttctgatatggcatggcagGTTTATGTCTGGAGCAAGCACAACCCTTTTATCCATATGAGCTTTCTGGGCCTGTTTACCTTTACGGCTGCGTACTTACCATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT