ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GCCTACCAAAATGAAGCTTCCACAGTTGGAACCAGATGAGAGAAGCGTGACAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctgggaccaaatcttctttctgagtatttgcgacaaatttactctctttatacgttattgtaggttgagttttgaattttttgaaccagtaga...

Basic information

species	Zea mays
transcript	GRMZM2G082181_T02
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G082181_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os04g47530.1 (Oryza sativa), 5'ss of exon 6

GCCTACCAAAATGAAGCTTCCACAGTTGGAACCAGATGAGAGAAGCGTGACAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctgggaccaaatctt---ctttctgagtatttgcgacaaatttactctct--ttatacg---ttatt-gtaggttgagttttgaat--------tttttgaaccagtaga---
 ||  ||||| |||||||||| ||||||||||||||||||||||||   ||||||||||||||||||||||| ||||| || || |||||||| |||||||||||| ||   | ||||||||    ||| ||| ||  |  |    ||||      |  ||| | |   ||||| | | ||   ||| ||           | |||  || | |  |   
ACCCGCCAAATTGAAGCTTCCGCAGTTGGAACCAGATGAGAGAAGCACAACAAACATAAAAGAAAGTGTTCGAGACTTCGTGGTTGGCAGTGGGGAATATgtgagttctacaaacaaatcttgccttttatgaatacatatgtttgatttttcacatggttacatgaacttattagcatgtgctgttgtgggccatcgtcctctttttactattctatag

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|32934688|gb|CF039500.1|CF039500

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|14245200|gb|BG873782.1|BG873782

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|26456358|gb|CA827941.1|CA827941

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|20802983|gb|BQ294033.1|BQ294033

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|32928770|gb|CF033582.1|CF033582

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|71770030|gb|DR967967.1|DR967967

EST:     TGTTCGGGGACTTTGTTGTCGGCAGTGGGGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: TGTTC-GGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|78544775|gb|DV622273.1|DV622273

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|22521216|gb|BU080027.1|BU080027

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|32837318|gb|CD976996.1|CD976996

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|87156516|gb|DY401305.1|DY401305

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|22521071|gb|BU079882.1|BU079882

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|32838904|gb|CD978585.1|CD978585

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|26558899|gb|CA831134.1|CA831134

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTTTCTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

EST: gi|16926375|gb|BM079443.1|BM079443

EST:     CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATAT                         GTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG
genomic: CAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAG

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: 91

GCCTACCAAAATGAAGCTTCCACAGTTGGAACCAGATGAGAGAAGCGTGACAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctg ... tctaaattagGTGATCAAAGATTTTAAGTTCACTGTTAACCAAGCAGTGCGACCAGTGGAGAAGCGCATTGATAAATTGATGAAAAAGAATGATAAGAGTAAGAAAAGCC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 93

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 113

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 95

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCCTACCAAAATGAAGCTTCCACAGTTGGAACCAGATGAGAGAAGCGTGACAAACATAAAAGAAAGTGTTCGGGACTTTGTTGTCGGCAGTGGTGAATATgtgagtgctgggaccaaatcttctttctgagtatttgcgacaaatttactctctttatacgttattgtaggttgagttttgaattttttgaaccagtaga

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA