ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgatcctgtgaatatgttgcaataaaatccaccgagtttcagactttttgtatattttgtcttgtcgatatattttaagaagttttgaaatttaatgcag

Basic information

species	Zea mays
transcript	GRMZM2G348675_T02
intron #	16
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G348675_T02 (Zea mays), 5'ss of exon 16
lower sequence: LOC_Os11g42420.1 (Oryza sativa), 5'ss of exon 16

TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgatcctgtga-atatgttgcaataaaatccaccgagtttcagactttttgtatattttgtcttgtcgatatattttaagaagttttgaaatttaatgcag
 |||||||| |||| |||||||||||| ||||||||||||||| |||||||||||||||   ||| ||||||||||| | ||||||||||||| ||||||| || ||||  || ||  ||| | ||||| ||||  ||  | ||| |||  ||| |  ||| |  | |  | ||||  || ||| |||  ||  |||||| | |||
CTTGCATACCATGTTCAAGCTCTTCCTGTCTGCTGTGGAGTATTTGCCATTCTCATCTGGAGATGCATCCAAGGCTTCTCTTGAAGAGATCATTGAGAGgtctgatgattatgggatgtatatggcaatgaaatgaacttattttgagatatttagcttatctgttttcatggataagttgtaacaagaatttcaatttactccag

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|71441451|gb|DR822501.1|DR822501

EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT

EST: gi|6526616|gb|AW215913.1|AW215913

EST:     TTCTCATCTGATAATGTATCCAAGGCTTGGTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT

EST: gi|21432148|gb|BQ547638.1|BQ547638

EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT

EST: gi|5555477|gb|AI881428.1|AI881428

EST:     GAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: GAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT

EST: gi|21843368|gb|BQ703949.1|BQ703949

EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT

EST: gi|86467221|gb|DY233591.1|DY233591

EST:     TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAG                         GGTGTTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT
genomic: TTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTT

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: 317

TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgat ... tttaatgcagGGTGCTTTCAAGATCTCGGCAAACAAAACCCACTAAGTATGATGGGGATTTCTCTGATGTTGCGCATCAACATCACCTGCAATCACTTCAAAAGGCTATG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 108

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 136

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 134

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTGCATACTATGTACAAGCTCTTCCTTTCTGCTGTGGAGTATCTGCCATTCTCATCTGATAATGTATCCAAGGCTTGTTTTGAAGAGATCATCGAGAGgtttgttgatcctgtgaatatgttgcaataaaatccaccgagtttcagactttttgtatattttgtcttgtcgatatattttaagaagttttgaaatttaatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA