ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccctgtcttgctatcaagatactttcgtgtgtttatatgccggtggatggtggttattcttgtagatttaccttattcggttatgtccctagt...

Basic information

species	Zea mays
transcript	GRMZM2G157443_T02
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157443_T02 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g02340.1 (Oryza sativa), 5'ss of exon 3

AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatg-caccctgtcttgctatcaagatactttcgtgtgtttatatgccggtggatggtggttattcttgtagatttaccttattcggttatgtccctagt--------
|||||||||||||||||||||||| |||||||||| |  |||||||| |||||||| ||| | |||||||| || || || ||||||||||| ||||||||||   |  || | |    | ||    | | | | ||      ||||||  ||    ||| || |   |||||||||   | |  |   | | || |  |         
AAGGCGGCCAACATCAAGGTCGAGGCCTACTGGCCCGGTCTCTTCGCCAAGCTCCTCGAGCACCGCAGCGTCGATGACCTCATCCTCTCCGTCGGATCTGgtaaaacctcccggccccttgtcccc-tgcctccttgc-----tatgccactgc---gtgattgtcgatgtagatttgattgaacctagtttatctcatgagggaaatt

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|211529784|gb|FL373525.1|FL373525

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGSGATCTG                         GTGGTGGCGCTGCTCCAGTTGCTGC
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCCAGTTGCTGC

EST: gi|211507235|gb|FL422061.1|FL422061

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTG                         GTGGCGGCGCTGCTCCAGTTGCTGCTTCCGCCCCA
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCA

EST: gi|211014153|gb|FL393610.1|FL393610

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTG                         GTGGTGGCGCTGCTCCAGTTGCTGCTTCCGC
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCCAGTTGCTGCTTCCGC

EST: gi|9794508|gb|BE552816.1|BE552816

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTG                         GTGGTGGCGCTGCTCC
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCC

EST: gi|211376384|gb|FL377804.1|FL377804

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTG                         GTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCAGCTGGGGGT
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCAGCTGGGGGT

EST: gi|8665846|gb|BE186662.1|BE186662

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTG                         GTGGTGGCGCTGCTC
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTC

EST: gi|211235863|gb|FL372783.1|FL372783

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTG                         GTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCAG
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCAG

EST: gi|211406019|gb|FL414976.1|FL414976

EST:     GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTG                         GTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCAGCTGGGGGTGCTGCAG
genomic: GCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCAGCTGGGGGTGCTGCAG

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: 509

AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccc ... tcgtttgtagGTGGTGGCGCTGCTCCAGTTGCTGCTTCCGCCCCAGCTGGGGGTGCTGCAGCTGCTGCTGCCCCTGCTGCAGAGGAGAAGAAGGAAGAGCCCAAGGAGGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 298

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 294

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 212

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGGCGGCCAACATCAAGGTCGAGTCCTACTGGCCGGCGCTCTTCGCTAAGCTCCTGGAGAAGCGCAGCGTTGAGGATCTAATCCTCTCCGTGGGATCTGgtatgcaccctgtcttgctatcaagatactttcgtgtgtttatatgccggtggatggtggttattcttgtagatttaccttattcggttatgtccctagt

- - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT