ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgcacatgtgcatgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag

Basic information

species	Zea mays
transcript	GRMZM2G020446_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 2

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgcacatgtgcatgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag
 || || |||||||||||||||||||||||||  ||||| |||| | |||| |||||||| |||||||||||  | ||||| |||||||||||||| ||||||  ||| | | ||   ||  |   || ||   | | || |    | |  | |      |  || ||    | || ||||  | |||||| |  || | |      
AGACAGTGAATTTGATTTGGAGAATATTGTCACTGCTGCGAGAGTTGCTGGGAAGAAAGTCCCTGTTTTGCTCAGGATAAACCCAGATGTGGATCCACAGgtaaagtttttc-ctcccacctcaggatacagtgggggatttagttatat-tggtatgctattgtgttattgtcatataat-actagaaatcagattatatag----

upper sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0070g00580.t01 (Vitis vinifera), 5'ss of exon 2

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatg-gttatcctctagtactccccaatgcacatgtg-catgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag
 ||||| |||||||||||||| |||||| |   ||||||||||  | |||| ||||| ||   |||||| ||| | || ||||||||||||||||| |||||||| | | || |    || | |  |    ||   |    |        |    |   || |||  |  |  ||   |||  |  |  ||||    || |        
TGATAGTGAATTTGATTTGGATAATATTATATCAGCTGCAAGAATTGCTGGCAAGAAGGTCAATGTTTTACTTAGGATCAATCCAGATGTGGATCCTCAGgtatgtgctgtcattgtttaattctaatgttacgaataatgtaatgttgtagggtgttcat-agaacaggtatttcccttaggttgggtaaatttggttat--------

upper sequence: GRMZM2G020446_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0038g04490.t01 (Vitis vinifera), 5'ss of exon 2

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgc-acatgtg-catgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag
 ||||| |||||||||||||| |||||| |   ||||||||||  | |||| ||||| ||   |||||| ||| | || ||||||||||||||||| ||||||||      | ||  |     | ||||  ||   |    |        |    |   || |||  |  |  |    |||  |  |  ||||    || |        
TGATAGTGAATTTGATTTGGATAATATTATATCAGCTGCAAGAATTGCTGGCAAGAAGGTCAATGTTTTACTTAGGATCAATCCAGATGTGGATCCTCAGgtatgtgctgtcactgtttaattctaatgttacgaataatgtaatgttgtagggtgttcat-agaacaggtattgcccttaggttgggtaaatttggttat--------

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|20208183|gb|BQ134272.1|BQ134272

EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC

EST: gi|148934359|gb|EC878388.2|EC878388

EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATC

EST: gi|211003081|gb|FL282330.1|FL282330

EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCACAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCCG
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCC-G

EST: gi|50329919|gb|CO525045.1|CO525045

EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCTTATGTTGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGC

EST: gi|9825116|gb|BE575318.1|BE575318

EST:     TAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC

EST: gi|26456264|gb|CA827847.1|CA827847

EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAG                         GTACATCCGCATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC

EST: gi|211452559|gb|FL415488.1|FL415488

EST:     GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCACAG                         GTACATCCGTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC

EST: gi|166441682|gb|EG195243.1|EG195243

EST:     CAGATGTGGATCCGCAG                         GTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC
genomic: CAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGC

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: 257

GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttat ... ttttcaacagGTACATCCTTATGTTGCCACGGGAAATAAAACGTCTAAATTTGGGATCCGCAATGAGAAATTGCAATGGTTTTTGGACTCTATCAAGTCATACCCGAATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATAGCGAATTTGATTTGGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTGCTTCGAATAAATCCAGATGTGGATCCGCAGgtatggttatcctctagtactccccaatgcacatgtgcatgtgcacacaaatagccaatgagagtatttggtttatttaattgcgagaaataaacttttttcaacag

- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG