ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTGCCAATTGAAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttttttatccttttataccgtcagttctcttttagtgttgctaatttaacaataataggctaatttgtgtgacctccctttctaaacacattt...

Basic information

species	Zea mays
transcript	GRMZM2G439457_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G439457_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os01g51220.1 (Oryza sativa), 5'ss of exon 7

AGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTGCCAATTGAAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttttttatccttttataccgtcagttctcttttagtgttgctaatttaacaataataggctaat-ttgtgtgacctccctttctaaacacattt-----
 || ||||| ||||||||||| |||||||||||||| |||||||||||||| ||||| ||||||||||| || |||||| ||||||| |||||||||||||||| || |  || |  || | |  |      | |||||     |   |||| ||| |   | ||   | | ||     ||    |||  || ||  |        
GGAAAATGCTGGCTTTCCTGCGGTAGTTACTGCACACTTTGTGCCAATTGAGGGCCAACAAAGGCCAAGGACAACAATCTTGATAAAATTTGCTGAAGAGgtaggagatgcttgtatttgtttttc------tttctttagaactatttaatataataggcacagttgactgttactgaacaatacttattagacttaaccaaata

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|12971087|gb|BG267308.1|BG267308

EST:     AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAG                         GTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA
genomic: AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA

EST: gi|18177651|gb|BM378861.1|BM378861

EST:     AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAG                         GTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA
genomic: AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA

EST: gi|23357590|gb|BU645239.1|BU645239

EST:     AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAG                         GTATTACCCAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACCCAAA
genomic: AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA

EST: gi|60339805|gb|DN206778.1|DN206778

EST:     AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAG                         GTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA
genomic: AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA

EST: gi|21759935|gb|BQ635476.1|BQ635476

EST:     AAGGCCAGCAAAGGCCCAGAACGACNATCCTGATAAAGTTTGCTGAAGAG                         GTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACCCAAA
genomic: AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA

EST: gi|22520635|gb|BU079446.1|BU079446

EST:     AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAG                         GTATTACCCAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACCCAAA
genomic: AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAA

EST: gi|161585639|gb|EY953311.1|EY953311

EST:     AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAG                         GTATTACACAG
genomic: AAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAG

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: 203

AGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTGCCAATTGAAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttt ... tttttttcagGTATTACACAGAGAAGCAAGACTGGGCTGAGTTTTTATGTATGTACACAAAACCTTTGACTAGCCTATTTGTAAGGTGAATCGTTACTGGAGTTTGGTGA

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 201

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 326

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 219

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGATAATGCCGGCTTTCCTGCCGTAGTTACTGCACATTTTGTGCCAATTGAAGGCCAGCAAAGGCCAAGAACGACAATCCTGATAAAGTTTGCTGAAGAGgtagaagttttttatccttttataccgtcagttctcttttagtgttgctaatttaacaataataggctaatttgtgtgacctccctttctaaacacattt

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aacaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cctccctt