ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttcctattacagttgcaataagcatatcatttttctgacatcatatctaacttgaaatgaatttttcag

Basic information

species	Zea mays
transcript	GRMZM2G034855_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G034855_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os01g21960.1 (Oryza sativa), 5'ss of exon 3

AAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttcctattacagttgcaataagcata----tcatttttctga-catcatatctaacttgaaatgaatttttcag--------------------------------------------------------------------------------------------------
| || ||||||||||| ||||| |||||||||||||||||||||||||| ||||||||||||||||||||||| ||||| || ||||||||||| |||||||| ||  |||| |  ||| |   |    |    |||| ||||  | |  ||| |   ||     | |||| ||                                                                                                      
AGGCCGAGAAGGAATTCAGAGTTGAAGTTGAGGCTATTGGTCATGTTCGCCACAAGAACTTGGTCCGGCTTCTGGGTTACTGTGTGGAGGGTACTCAAAGgta-ttgatatttctcttgtatctattgcaatgttcatatttccaagctacatgtactaccaagcaagaatattcttctagacattccatgctctctgagacctctaggttcatttgactgcaatacttgtatggaattctaagacatatttgttaactttgtgtgcttttttcag

upper sequence: GRMZM2G034855_T02 (Zea mays), 5'ss of exon 3
lower sequence: AT5G18500.1 (Arabidopsis thaliana), 5'ss of exon 3

AAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgta-gttcctattacagttgcaataagcata-tcatttttctgacatcatatctaacttgaaatg----aatttttcag---
||||||| || || || ||||| |||||||| ||||| ||||| |||||||| || ||||||||||| ||||| || |||||  |||| || || || ||||| ||   |  |   |||| |  |     | |  || ||||||  |   |   ||| | |||||    ||   || |    
AAGCTGATAAAGACTTCAGAGTTGAAGTTGAAGCTATAGGTCACGTTCGACATAAAAACTTGGTCCGCCTTCTCGGATATTGTATGGAAGGAACGCAGAGgtatgtatgttctgttgttgaatgatctgcagtttttcttctgaattttcactaaacatcaaatgcggtaacacttaattag

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|87157535|gb|DY402324.1|DY402324

EST:     CACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAG                         GATGCTTGTCTATGAGTATGTGAACAATGGAAACCTAGAACAAGGGCTTCA
genomic: CACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttccta ... aatttttcagGATGCTTGTCTATGAGTATGTGAACAATGGAAACCTAGAACAATGGCTTCA

EST: gi|211042367|gb|FL052105.1|FL052105

EST:     CACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAG                         GATGCTTGTCTATGAGTATGTGAACAATGGAAACCTAGAACAATGGCTTCA
genomic: CACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttccta ... aatttttcagGATGCTTGTCTATGAGTATGTGAACAATGGAAACCTAGAACAATGGCTTCA

EST: gi|60397397|gb|DN230213.1|DN230213

EST:     ACAAGAATTTGGTCCGGCTTTTTGGTTATTGGGTGGAGGGTACCCAAAG                         GATGCTGGTCTATGAAGTATTGTGAACAATGGAAACCTAGAACAATGGCTT
genomic: ACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttccta ... aatttttcagGATGCTTGTCTATG-AGTA-TGTGAACAATGGAAACCTAGAACAATGGCTT

EST: gi|211042366|gb|FL052104.1|FL052104

EST:     CACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAG                         GATGCTTGTCTATGAGTATGTGAACAATGGAAACCTAGAACAATGGCTTCA
genomic: CACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttccta ... aatttttcagGATGCTTGTCTATGAGTATGTGAACAATGGAAACCTAGAACAATGGCTTCA

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), 48 (downstream exon)
Score: 208

AAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttccta ... aatttttcagGATGCTTGTCTATGAGTATGTGAACAATGGAAACCTAGAACAATGGCTTCATGGAGCTATGAGTCAACATGGCTCTCTTACATGGGAGGCCCGCATAAAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 246

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 140

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 541

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGCTGAGAAGGAATTTAGAGTAGAAGTTGAGGCTATTGGTCATGTTCGACACAAGAACTTGGTCCGGCTTCTTGGTTATTGCGTGGAGGGTACCCAAAGgtagttcctattacagttgcaataagcatatcatttttctgacatcatatctaacttgaaatgaatttttcag

- - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG