ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaacaaaatgatatctcgattcatgtgaaaaaactgtctatttattgtcactttttgtaaaattcag

Basic information

species	Zea mays
transcript	GRMZM2G116087_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G116087_T03 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os01g55870.1 (Oryza sativa), 5'ss of exon 5

GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaaca----aaatgatatctcg-------------attcatgtgaaaaaactgtctattt------------attgtcactttttgtaaaattcag
|| ||||||||||| || |||||||| ||||||||||||||||| |||||||||||||| ||||||||||||| ||| || |||||||| || || |||| || ||||        || | | | |||||    |      |  | |    |  || | ||| |              | ||| | |||     |||||||             ||| |   | | ||  || |||||
GCGCTCTCCAAAAGAATTCACTATGGTAAGTTTGTGGCAGAGGCTAAGTTTCAAGAGTCTCCTGAAGCTTACATGCCTGCGATAATAGCACAGgtttgtg-ttctgttttgctgtataatctgtctttatcatgggaagcaaataaattccatgtgttttcttgtacattactttaggtacatatcaaagttgagtctattatgcaagcggctaattatttttatctgggaatttcag

upper sequence: GRMZM2G116087_T03 (Zea mays), 5'ss of exon 5
lower sequence: GLYMA01G06660.1 (Glycine max), 5'ss of exon 4

GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaacaaaatgatatctcgattcatg-tgaaaaaactgtctatttattgtcactttttgtaaaattcag
|| ||||| ||||| ||||||||||| || ||||| || ||||| |||||||||||  |||||   |  ||     | |||||   |||  ||||     ||||||        |||  | || ||||   |     ||  |||     |  |||  |   ||  || ||  | |    || ||   |                      
GCTCTCTCAAAAAGAATCCACTATGGCAAATTTGTTGCTGAGGCAAAGTTTCAAGATGCCCCTTCTGAATATGTAGCTGCCATTGAAGCGAAAgt--aaacttttgcatacctgattcattttattttccattgtgattctagat----accatacttaattttctgatgctacattaatccatgcttcacag-----------------

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|148961521|gb|EE012273.2|EE012273

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|78125597|gb|DV543981.1|DV543981

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|78089259|gb|DV517633.1|DV517633

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|149086679|gb|EE176219.2|EE176219

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|149029769|gb|EE154771.2|EE154771

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|211039898|gb|FK958023.1|FK958023

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|71762890|gb|DR960827.1|DR960827

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|149033875|gb|EE155016.2|EE155016

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTTTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|60356414|gb|DN223387.1|DN223387

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|148957418|gb|EC903477.2|EC903477

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGGTGGAGCGTGC
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGG-TGGAGCGTGC

EST: gi|31352097|gb|CD436454.1|CD436454

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCT

EST: gi|211304785|gb|FL143334.1|FL143334

EST:     CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAA                         GACCGTGATCA
genomic: CCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCA

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: 62

GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgctt ... taaaattcagGACCGTGATCAACTCATGCGCCTTCTCACATATGAAACGGTGGAGCGTGCTGTCGAACACAGGGTGGAAGCCAAAGCCAAGATCTTCGGGCAAGAGGTGA

Block sizes: 49 (upstream exon), 24 (downstream exon)
Score: 68

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 55

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 368

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCACTCTCCAAAAGGATCCACTATGGGAAGTTTGTGGCAGAGGCCAAGTTTCAAGAGTCCCCTGAAGCTTACACGCCAGCCATAATAGCCCAAgtctgtgcttttgttccaactattagtatttttttatttcagagtttcagaacaaaatgatatctcgattcatgtgaaaaaactgtctatttattgtcactttttgtaaaattcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC