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

gtaaggatctcacatccccggatctcgattccctggcggcgtccagcgctgatcgagtgccggtggtcgcttgggtgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG

Basic information

species	Zea mays
transcript	GRMZM2G064753_T01
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G064753_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os01g42650.1 (Oryza sativa), 3'ss of exon 1

--------------gtaaggatctcacatccccggatctcgattccctggcggcgtc----cagcgctgatcgagtgccggtggtcgcttgggtgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG
                  ||||||| | |    |||| | | |||| ||| |  ||     | ||||||||||   | ||||||| |   ||  | ||||||||||||||||||||||  |||||||||||||||||||||||||||||||| ||||| |||||||| | ||| |||||||||
gtaagggctctcctcctcggatctcgcgtgtttggatgt-gcttccgtggggtggtgggggcggcgctgatcg---gtcggtggttggg-ggtcgcgctgcagGGGACAAGCCGGCGACGGTGGAGGACGTCATGCCCATCGCCACGGGGCTGGAGCGCGAGGAGCTCGCGGCGGAGCTCAAG

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|211282257|gb|FL038859.1|FL038859

EST:     GCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCTCAG                         GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG
genomic: GCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG

EST: gi|60341353|gb|DN208326.1|DN208326

EST:     CCGCTCCTCTCAG                         GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG
genomic: CCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG

EST: gi|211158395|gb|FK955819.1|FK955819

EST:     CTCTCCTCGGCGGCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCGTCAG                         GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGNCTC
genomic: CTCTCCTCGGCGGCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTC-TCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTC

EST: gi|211161585|gb|FK955846.1|FK955846

EST:     GCTCTCCTCGGCGGCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCTCAG                         GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG
genomic: GCTCTCCTCGGCGGCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG

EST: gi|211282259|gb|FL038861.1|FL038861

EST:     GCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCTCAG                         GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG
genomic: GCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG

EST: gi|44901526|gb|CK828071.1|CK828071

EST:     TCCGCCGCACCAGCCCGCTCCTCTCA-                         CGTTCAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG
genomic: TCCGCCGCACCAGCCCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG

EST: gi|101401431|gb|EB822393.1|EB822393

EST:     CGCTTTCCGCCGCACCAGCCCGCTCCTCTCAG                         GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG
genomic: CGCTTTCCGCCGCACCAGCCCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG

EST: gi|60398986|gb|DN231802.1|DN231802

EST:     CCGCTCCTCTCAG                         GGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG
genomic: CCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCG

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), 49 (downstream exon)
Score: 81

GCCGCCGGGGCCCCTGCGGCGTCCGCCTCCTCTGCAGCCCGCGCCGCCCCGCTCTCCTCGGCGGCCGCCGCTTTCCGCCGCACCAGCCCGCTCCTCTCAGgtaaggatct ... tgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 63

Block sizes: 35 (upstream exon), 49 (downstream exon)
Score: 34

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 37

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ccctggcggcgtccagcgctgatcgagtgccggtggtcgcttgggtgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG

                cgctgat  putative branch site (score: 37)

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaggatctcacatccccggatctcgattccctggcggcgtccagcgctgatcgagtgccggtggtcgcttgggtgtgctgcagGGGACAAGCCGGCGAGTGTGGAGGACGTCATGCCCATCGCCACGGGGCTCGAGCGGGAGGAGCTGGAGGCCGAGCTCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA