ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

...tcggtatttaccaacctggatcaatttatatcgtatacgtataccatatgggaaatgtcttcatagctgtgggttgtcttatggctccttgaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAAGAGTTGCTCAACAATGGACACTGGCTGCCTGTCATCTATGAATATTACT

Basic information

species	Zea mays
transcript	GRMZM2G410515_T02
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G410515_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 1

---tcggtatttaccaacctggatcaatttatatcgtatacgtataccatatgggaaatgtcttcatagctgtgggttgtcttatggctcct--tgaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAAGAGTTGCTCAACAATGGACACTGGCTGCCTGTCATCTATGAATATTACT---
   | | ||  |    |    |||  | | |||     |   |       ||   ||| |  ||  |   | | |  ||| | |||| ||||  ||  |||||||  |       || | |||| |   || |||| ||||     | ||||    ||||||||  |  ||||| ||||||||||||||||||||||| || |||   
aacttgataaatttacatactgatacagtgatact---tggctgactttcataacaaacggttttgtg--tattgtgtgtttaatggttcctcttgtttttgcagACGCTCTTGCGTGCTTATTTGTCAAATCAGATCTGAATATAATTTTA---GGAGTTGCTTCAGCATGGATACTGGCTGCCTGTCATCTATGAACATAACTGGA

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|91056859|gb|EB167277.1|EB167277

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211005246|gb|FL018196.1|FL018196

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGAAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211002473|gb|FL018192.1|FL018192

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGAAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211417844|gb|FL018174.1|FL018174

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGAAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211417848|gb|FL018178.1|FL018178

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGAAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211417840|gb|FL018170.1|FL018170

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGAAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|89248325|gb|DY620111.1|DY620111

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211002465|gb|FL018184.1|FL018184

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAA-AGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211417841|gb|FL018171.1|FL018171

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGAAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|74236167|gb|DT644081.1|DT644081

EST:     CTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA
genomic: CTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

EST: gi|211002466|gb|FL018185.1|FL018185

EST:     CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCG                         TAGTCTGCCTGTACCTATTGGCTGAAGAAGAGCTGACCCCCACTTTATCAA
genomic: CCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAA

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: 47 (upstream exon), 42 (downstream exon)
Score: 55

CGTACACACCCAATTCCTCGCAACTGGGCTCCCCCGCCTCCACGACACTGCCCCCCGCCTCAAGTCCGCCGCCTCCATTCTTCAGCTCTCCTATCCTCCGgtgagtagcc ... gaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAAGAGTTGCTCAACAATGGACACTGGCTGCCTGTCATCTATGAATATTACT

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 203

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 84

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 151

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

atatgggaaatgtcttcatagctgtgggttgtcttatggctccttgaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAAGAGTTGCTCAACAATGGACACTGGCTGCCTGTCATCTATGAATATTACT

                                       ctccttg  CT-rich tract
                                           ttgaattt  TA-rich tract

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tcggtatttaccaacctggatcaatttatatcgtatacgtataccatatgggaaatgtcttcatagctgtgggttgtcttatggctccttgaatttgcagTAGTCTGCCTGTACCTATTGGCTGAAGCAGAGCTGACCCCCACTTTATCAAGAGTTGCTCAACAATGGACACTGGCTGCCTGTCATCTATGAATATTACT

- - - - - - - -ctggatc
- - - - - - - - - - - - - - - - - - - - - -ccatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agctgtg