ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaattgtttgttctttatatatttttgggtattttcttttctccaaacaagtttaccttaatattttgagtctctaagttatttggttcaacct...

Basic information

species	Zea mays
transcript	GRMZM5G871463_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G871463_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os08g32620.2 (Oryza sativa), 5'ss of exon 3

CAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaattgtttgttctttat-atattt-ttgggtattttcttttctccaaacaagtttaccttaatattttgagtctctaagttatttggttcaacct--
|||||| |||||||||||||| |||||||| ||| |||| ||||| ||| ||||||||| |||| ||||||||||   |||| |||| | |||||||||||| ||    || |||  | | ||| ||||   |||  |||||   ||| ||   | ||   || || | | |||    | |  || ||| |    | |   |  
CAAAAAACTAGATCACTTTGTGTGCTCAGATTGTGTCAAGGAAAACGGTGCAAAGAGACCTTCACATGCATATGCAGGTTCAACAAAGTATGAGCCTAAGgtgagcctcttcttttctatatattatatgggttgattatttatatttttctgtagaaagatagct-agtttttc---ttttgaaattaatattattattgtga

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|211293088|gb|FL433983.1|FL433983

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

EST: gi|78022938|gb|DV491325.1|DV491325

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

EST: gi|37376233|gb|CF624624.1|CF624624

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

EST: gi|37379451|gb|CF626469.1|CF626469

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

EST: gi|60355176|gb|DN222149.1|DN222149

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

EST: gi|211377790|gb|FL432886.1|FL432886

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGCAG                       
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCT-A--AGgtaagttaat ... acaactgc

EST: gi|78544163|gb|DV621661.1|DV621661

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

EST: gi|40334533|gb|CK368603.1|CK368603

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACCAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

EST: gi|5152847|gb|AI759012.1|AI759012

EST:     CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAG                         GCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT
genomic: CAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCAT

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: 273

CAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaat ... acaactgcagGCTGAACCAAAAAGGCAGAGGAGGTAACAAACTGTGAGTGGTAACATCCATATGGGTAAGGGGAGATGTGCTGCTTCTGTGGTGAATCAGCCCTTGCCCT

Block sizes: 46 (upstream exon), 49 (downstream exon)
Score: 126

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 192

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 147

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAAAAAGCTAGATCACTTTGTTTGCTCAGACTGTTTCAAAGAAAATGGTTCAAAGAGACTTTCAAATGCATATGCCACTTCACCAAATTTTGAGCCTAAGgtaagttaattgtttgttctttatatatttttgggtattttcttttctccaaacaagtttaccttaatattttgagtctctaagttatttggttcaacct

- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA