ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

ACCAAGCCCGGTTCCACGCACACCAGTGTGCAGGGGGTCTTTGCAGCTGGGGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagcttcattgttgttttaatgctgctgtttaggtattccatgatcccaatagtgatttgcttatggatcatgccatgctgcatccatgccatgct...

Basic information

species	Zea mays
transcript	GRMZM5G841142_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G841142_T02 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os06g22140.1 (Oryza sativa), 5'ss of exon 1

ACCAAGCCCGGTTCCACGCACACCAGTGTGCAGGGGGTCTTTGCAGCTGGGGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagcttcattg-ttgttttaatgctgctgtttaggtattccatgatcccaatagtgatttgctta--tggatcatgccatgctgcatccatgccatgct
||||||||||| ||||| |||||||| ||  |||| ||||| || || || ||||| |||||||||||||| ||||||||||||||||| || ||||||||||||    |||  | ||||  ||   |    || | | |   |  |  |  | || |     |  | |  | ||| || |     ||||   |     ||  
ACCAAGCCCGGCTCCACTCACACCAGCGTCAAGGGAGTCTTCGCCGCCGGTGATGTTCAGGACAAGAAGTATCGCCAGGCCATTACTGCCGCGGGATCAGgtatactactcaaagcttgtaataccaccagagtat-gatgcacatttgtggcgattggagcatattgactttgataattcagcaatgcaattacttggtg--

upper sequence: GRMZM5G841142_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA11G09350.1 (Glycine max), 5'ss of exon 1

ACCAAGCCCGGTTCCACGCACACCAGTGTGCAGGGGGTCTTTGCAGCTGGGGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagcttcattgttgttttaatgctgctgtttaggtattccatgatcccaatagtgatttgcttatggatcatgcc--atgctgcatccatgccatgct-------
|| ||||| ||  | ||| | ||||||||| |||| || ||||| ||||||||||| ||||||||||||||  | || || |||||||| |||||  | ||||       | |||| | ||||     | ||  |||   ||  ||    |  || |   | ||  | |  || || ||   |  || | |   |  ||| |       
ACGAAGCCGGGGACGACGAAGACCAGTGTGGAGGGAGTGTTTGCTGCTGGGGATGTTCAGGACAAGAAGTATAGGCAAGCTATTACTGCTGCTGGCACTGgta-------cgttgtagatttatctaagatgcgtagagtttttattggac--attgctgtatgtgtgtatatgatccctggttttgaagcgtagttatgttttgtcca

upper sequence: GRMZM5G841142_T02 (Zea mays), 5'ss of exon 1
lower sequence: GLYMA01G36070.1 (Glycine max), 5'ss of exon 1

ACCAAGCCCGGTTCCACGCACACCAGTGTGCAGGGGGTCTTTGCAGCTGGGGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagcttcattgttgttt-taatgctgctgtttaggtattccatgatcccaatagtgatttgcttatggatcatgccatgctgcatccatgccatgct----
|| ||||| ||  | ||| | ||||||||  |||| || ||||| ||||||||||| ||||||||||||||  | || || |||||||| |||||  | ||||  || | ||   |||| | | ||||       |   ||||  |  ||     ||   |  ||  | || || |   |   |||  |      |||  |    
ACGAAGCCGGGGACGACGAAGACCAGTGTTGAGGGAGTGTTTGCTGCTGGGGATGTTCAGGACAAGAAGTATAGGCAAGCTATTACTGCTGCTGGCACTGgta--agttacagatttgtctatgatgcatagagctgcttattggac-attggtgtatgtacatgtgtgtgtataagatc--cctggttttgaagcatagtagtg

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|74246375|gb|DT654289.1|DT654289

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|76014373|gb|DT941543.1|DT941543

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|110518037|gb|EE022624.1|EE022624

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|93011797|gb|EB637317.1|EB637317

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|32918282|gb|CF023094.1|CF023094

EST:     GGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|30307059|gb|CD001732.1|CD001732

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|78117600|gb|DV535987.1|DV535987

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|94480296|gb|EB709254.1|EB709254

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|211244715|gb|FL479518.1|FL479518

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|211425417|gb|FL239290.1|FL239290

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|78073901|gb|DV502335.1|DV502335

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|86474978|gb|DY241348.1|DY241348

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|71760597|gb|DR958534.1|DR958534

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|30306429|gb|CD001102.1|CD001102

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|86473113|gb|DY239483.1|DY239483

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|88748315|gb|DY532456.1|DY532456

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

EST: gi|50322856|gb|CO517982.1|CO517982

EST:     GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAG                         GTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC
genomic: GGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCAC

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: 46 (upstream exon), 46 (downstream exon)
Score: 28

ACCAAGCCCGGTTCCACGCACACCAGTGTGCAGGGGGTCTTTGCAGCTGGGGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagctt ... gatggtccagGTTGCATGGCTGCTCTGGATGCAGAGCACTACCTGCAGGAGGTTGGAGCACAGGAAGGGAAGACCGATTGACTATGTCTGGGCCAAGCTGCTCTTGGGCC

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

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

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 52

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACCAAGCCCGGTTCCACGCACACCAGTGTGCAGGGGGTCTTTGCAGCTGGGGATGTCCAGGACAAGAAGTACCGCCAGGCCATTACTGCAGCTGGATCAGgtataagcttcattgttgttttaatgctgctgtttaggtattccatgatcccaatagtgatttgcttatggatcatgccatgctgcatccatgccatgct

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA