ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatatttcagaataatgttactagttggttttaagtagaaatgctcatttctgaacttggcgctgaactggctctgggattgaccataccatatgca...

Basic information

species	Zea mays
transcript	GRMZM2G027821_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G027821_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g06120.3 (Oryza sativa), 5'ss of exon 6

GGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatatttcagaataatgttactagttggttttaagtagaaatgctcatttctgaacttggcgctgaactggctctgggattgaccataccatatgca------
||| || ||||||||||||||||| || ||||| ||||| |||||||| ||||| || |||||||| ||||||||||||||||||||| |  | |||||||||||| || | |     |  ||   ||||    |   |     | |    ||||     |   |  ||| ||  ||      ||||| ||| || || |      
GGAAGCATGCAATGATATTATGGCATATTCCCTGATATTATCCTGCTGTTGTTACACTTGCTGTGTGAGGAGAAAGCTTCGTCAAAAGCTAAATATTGCGgtaaattttcctgtcccttcatatctgttgtcaattgattttttttcctgcttct----ctaaagtagaagtgcttc--attctgaccctacaatgtgaaactgag

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|6022374|gb|AW067302.1|AW067302

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|211064881|gb|FL464879.1|FL464879

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|60357315|gb|DN224288.1|DN224288

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|88757593|gb|DY541734.1|DY541734

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|211190398|gb|FL318556.1|FL318556

EST:     GTTATACATGCTGTGTAAGGAGGAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|211064880|gb|FL464878.1|FL464878

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|74235248|gb|DT643162.1|DT643162

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|32847753|gb|CD987434.1|CD987434

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGTG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|71434265|gb|DR815315.1|DR815315

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|78078285|gb|DV506700.1|DV506700

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATTTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|211067604|gb|FL464880.1|FL464880

EST:     AGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: AGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

EST: gi|71328372|gb|DR800816.1|DR800816

EST:     GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCG                         GGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG
genomic: GTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCG

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: 123

GGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatattt ... ttctgaacagGGAGGCTGCTGTGACGACTTCCTTTCACATCTGCTGTGTTGTTGCTGCGCGCTTGTTCAAGAATGGCGGGAAGTTGAGATTCGCGGAGCTTATA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 50

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 29

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 77

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGAGGCTTGCAATGATATTATGGCGTACTCCCTAATATTGTCCTGCTGCTGTTATACATGCTGTGTAAGGAGAAAGCTTCGTCAAAAGTTGGACATTGCGgtaaatatttcagaataatgttactagttggttttaagtagaaatgctcatttctgaacttggcgctgaactggctctgggattgaccataccatatgca

- - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cagaataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagtagaa