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

gtgagtctttccctccctcccttcgtgtgtggtggtctgctgatatgaagaatttggtttccctgtctcactagaacactatcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCAC

Basic information

species	Zea mays
transcript	GRMZM2G131249_T03
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g06330.1 (Oryza sativa), 3'ss of exon 4

gtgagtctttccctccctcccttcgtgtgtggtggtctgctgatatgaagaattt-ggtttccctgtctcactagaacactatcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCAC
|| ||||| || ||| |    ||| ||||  |||     ||||| | ||||||||   || |   |||||||||  |   |||| ||||||||||||||| | ||||||||| |||||||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||| ||||| 
gttagtctatctctctcatg-ttcatgtgcagtg-----ctgattttaagaattttaattgcatggtctcactatgatgatatcttttcagAGAAACAGGGATAGTTAAGCTAAAAATGCAAGGTGCCTGCAGTGGATGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTCATGCAT

upper sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ28518 (Selaginella moellendorffii), 3'ss of exon 3

gtgagtctttccctccctcccttcgtgtgtggtggtctgctgatatgaagaatttggtttccctgtctcactagaacactatcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCAC
                      |   || |     |||  |   | ||| ||||              |  |      ||   |  |||| ||  | || |  ||  ||||||| ||||||||||| ||||| ||||||||||| ||| | || ||  | |||||||| || ||||||||||| ||||| 
---------------------gtaaagtttctatatct-ttctcaagaaaaattcaaaaaggtaaatccttttttcttctcgtcgatcagGGAGTCCGGGATCGTGGAGCTTAAGATGCAAGGTGCTTGCAGTGGCTGTCCAAGCTCGGCCGTGACGCTTAAGTCTGGAATCGAAAACATGCTCATGCAT

upper sequence: GRMZM2G131249_T03 (Zea mays), 3'ss of exon 4
lower sequence: EFJ30409 (Selaginella moellendorffii), 3'ss of exon 3

gtgagtctttccctccctcccttcgtgtgtggtggtctgctgatatgaagaatttggtttccctgtctcactagaacactatcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCAC
                     |     |    | || | ||     ||| ||||      ||   | ||         ||   |  |||| ||  | || |  ||  ||||||||||||||||||| ||||| ||||||||||| ||| | || ||  | |||||||| || ||||||||||| ||||| 
--------------------gtaaagtttctatagttttct--cgagaaaaattcaaacccctcctttctt-------ctcgtcgatcagGGAGTCCGGGATCGTCGAGCTTAAAATGCAAGGTGCTTGCAGTGGCTGTCCAAGCTCGGCTGTGACGCTTAAGTCTGGAATCGAAAACATGCTCATGCAT

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|211501968|gb|FL391661.1|FL391661

EST:     GCTNGTTCAAGATGACNGGCGGTGACATTGAATACCGNAGGATTCGACCC                         AGAAACAGGAACAGTTAAGCTTTAAAATGCAAGGTGCCTGCAGCGGGCTGT
genomic: GCT-GTTCAAGATGAC-GGCGGTGACATTGAATACCG-AGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTT-AAAATGCAAGGTGCCTGCAGCGG-CTGT

EST: gi|67024319|gb|CO453068.1|CO453068

EST:     CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCC                         AGAAACAGGAACAGTTAAGCTTTAAATGCAGGGTGCCTGCAGCGGCTGTCC
genomic: CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC

EST: gi|38502507|gb|CF972367.1|CF972367

EST:     CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCC                         AGAAACAGGAACAGTTAAGCTTAAAATGCAAGGGGCCTGCAGCGGCTGTCC
genomic: CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC

EST: gi|71436813|gb|DR817863.1|DR817863

EST:     CCAGCTGTTCAAGATGACGGCGGGGACATTGAATACCGAGGATTCGACCC                         CGAAACAGGAACAGTTAACCTTAAAATGCCAAGGGGCCT
genomic: CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGC-AAGGTGCCT

EST: gi|76012527|gb|DT939697.1|DT939697

EST:     CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCC                         AGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC
genomic: CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC

EST: gi|94475082|gb|EB704040.1|EB704040

EST:     CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCC                         AGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC
genomic: CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC

EST: gi|211452112|gb|FL393956.1|FL393956

EST:     CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCC                         AGAAACAGGAACAGTGTA-GCTTAA
genomic: CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGT-TAAGCTTAA

EST: gi|84980471|gb|DW530820.1|DW530820

EST:     CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACTAAGGATTCGACCC                         AGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC
genomic: CCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCC

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: 48 (upstream exon), 47 (downstream exon)
Score: 164

ATTCTGAAATAGTTGCCATGATAAAAGAATTATTGGAGACTCGTATTCGACCAGCTGTTCAAGATGACGGCGGTGACATTGAATACCGAGGATTCGACCCgtgagtcttt ... atcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCAC

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 191

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 286

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tctgctgatatgaagaatttggtttccctgtctcactagaacactatcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCAC

                             gtctcac  putative branch site (score: 286)
                                           ctatcctttc  putative PPT
            aagaattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagtctttccctccctcccttcgtgtgtggtggtctgctgatatgaagaatttggtttccctgtctcactagaacactatcctttcagAGAAACAGGAACAGTTAAGCTTAAAATGCAAGGTGCCTGCAGCGGCTGTCCAAGTTCGTCAGTCACATTGAAGTCTGGGATAGAAAACATGCTTATGCAC

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