ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CGGGGACGTCGGCGGGGGAGAGGAAGCTAATGCCGACGATCGAGGACGAGCTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatgaaccactaatcctccgttctatacgccttaatcaatttgttttccgtcatcggtgtcctccctacgtcatggatatatgtatatatattc...

Basic information

species	Zea mays
transcript	GRMZM2G033359_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G033359_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os01g55940.1 (Oryza sativa), 5'ss of exon 2

CGGGGACGTCGGCGGGGGAGAGGAAGCTAATGCCGACGATCGAGGACGAGCTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatgaaccactaatcctccgttctatacgccttaatcaatttgttttccgtcatcggtgtcctccctacgtcatggat--atatgtatatatattc
||||||| |||||||||||||||||||||||||||||||| || || |||||  ||||| | ||||||||||||||||| |||||||||||||||||| ||||||||||  | | || |  ||| |  |  ||   | || |  |    | |  |    |   | | ||| | | | | | |||    | || |   |    
CGGGGACTTCGGCGGGGGAGAGGAAGCTAATGCCGACGATAGAAGATGAGCTGGACAGGAGGCAGATGCTCTACAGCCTCCTCATGCCCGTCATGAACTTgtgggtgatccatctctgaatctctggccattat--cctactttagccatctaactgttttctttttctcaccatgcctttgattgggacgttttcttgact

upper sequence: GRMZM2G033359_T01 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0091g00310.t01 (Vitis vinifera), 5'ss of exon 2

CGGGGACGTCGGCGGGGGAGAGGAAGCTAATGCCGACGATCGAGGACGAGCTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatgaaccactaatcctccgttctatacgccttaat-caatttgttttccgtcatcggtgtcctcccta-cgtcatggatatatgtatatatattc
| ||||| || || || |||||||| || ||||| || ||  | || ||| |  |  | || |||||||||||||||||||||||||| || |||||| |||  |||  |||     ||   | |||| || |  |  |||| |  | |  ||   |  |   | ||  | |  | ||  || | | |     |  |     
CTGGGACATCAGCTGGTGAGAGGAAACTCATGCCCACTATTCAAGAAGAGTTGGATCGTCGTCAGATGCTCTACAGCCTTCTCATGCCTGTAATGAACTTgtaagtggagaa-----aaagatgcgttttagatactctaattctgtgtcgttattgagaagagcgtttttctaaacgaaattgctttcctattgcag----

upper sequence: GRMZM2G033359_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ23432 (Selaginella moellendorffii), 5'ss of exon 2

CGGGGACGTCGGCGGGGGAGAGGAAGCTAATGCCGACGATCGAGGACGAGCTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatgaaccactaatcctccgttctatacgccttaatcaatttgttttccgtcatcggtgtcctccctacgtcatggatatatgtatatatattc
|||| |||||||| ||  ||||||| || ||||| || |||  ||| ||  || |  | |||    ||||||||||||| ||||||||||| ||||||| ||| |||         |  ||    | |  ||    ||  | | |    ||  |    |   |||    | || ||                        
CGGGAACGTCGGCTGGCCAGAGGAAACTCATGCCCACCATCTCGGAAGAATTCGAGCGCCGCTGCCTGCTCTACAGCCTCCTCATGCCCGTGATGAACCAgtgagtg---------tggtctcgagcttgatcgcgctcgagctagcgattgacaa--actcgtgcatgcgctgcgcag---------------------

upper sequence: GRMZM2G033359_T01 (Zea mays), 5'ss of exon 2
lower sequence: EFJ25415 (Selaginella moellendorffii), 5'ss of exon 2

CGGGGACGTCGGCGGGGGAGAGGAAGCTAATGCCGACGATCGAGGACGAGCTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatgaaccactaatcctccgttctatacgccttaatcaatttgttttccgtcatcggtgtcctccctacgtcatggatatatgtatatatattc
|||| |||||||| ||  ||||||| || ||||| || |||  ||| ||  || |  | |||    ||||||||||||| ||||||||||| ||||||| ||| |||         |  ||    | |  ||    ||  | | |    ||  |    |   |||    | || ||                        
CGGGAACGTCGGCTGGCCAGAGGAAACTCATGCCCACCATCTCGGAAGAATTCGAGCGCCGCTGCCTGCTCTACAGCCTCCTCATGCCCGTGATGAACCAgtgagtg---------tggtctcgagcttgatcgtgctcgagctagcgattgacaa--actcgtgcatgcgctgcgcag---------------------

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|76284302|gb|DV023870.1|DV023870

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|74243210|gb|DT651124.1|DT651124

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|149072890|gb|EE161146.2|EE161146

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATNCA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCAT-CA

EST: gi|148991587|gb|EE033115.2|EE033115

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|89762876|gb|DY690300.1|DY690300

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|78104682|gb|DV523100.1|DV523100

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|76289269|gb|DV028837.1|DV028837

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|71317423|gb|DR795426.1|DR795426

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|78108699|gb|DV527117.1|DV527117

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|76933890|gb|DV173628.1|DV173628

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|149103010|gb|EE288370.2|EE288370

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|149078141|gb|EE166889.2|EE166889

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|78080653|gb|DV509065.1|DV509065

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

EST: gi|76018817|gb|DT945987.1|DT945987

EST:     CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCT                         GTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA
genomic: CTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAA

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: 27 (upstream exon), 23 (downstream exon)
Score: 1

CGGGGACGTCGGCGGGGGAGAGGAAGCTAATGCCGACGATCGAGGACGAGCTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatg ... tgttcatcagGTACGTGCCTGGGCTGGACAAGGGCAAGGGCCTCTACTTCCTGTTCATCAAGTCGGAGACGAAGACGCCCGGGGGGCTCCCGGCGCGCCCCGTGCTGACC

Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 25

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 55

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 92

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGGGGACGTCGGCGGGGGAGAGGAAGCTAATGCCGACGATCGAGGACGAGCTCAACAGGCGCCAGATGCTCTACAGCCTTCTCATGCCCGTCATGAACCTgtgggtgatgaaccactaatcctccgttctatacgccttaatcaatttgttttccgtcatcggtgtcctccctacgtcatggatatatgtatatatattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctccctac