ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

CAGTAACTACGTCTCTGTTGGTGCCTCTGGGGCTTTGTTTGGCCTCCTTGGATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaaagtgtattacgtgtgtactgttttgctctagtttttctctctgttttttttggctaagtttcagtcaattcgttcctgcag

Basic information

species	Zea mays
transcript	GRMZM2G157384_T01
intron #	3
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G157384_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os08g43320.1 (Oryza sativa), 5'ss of exon 3

CAGTAACTACGTCTCTGTTGGTGCCTCTGGGGCTTTGTTTGGCCTCCTTGGATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaaagtgtattacgtgtgtactgttttgctctagtttttctctctgttttttttggctaagtttcagtcaattcgttcctgcag
 | ||||||| |||| |||||||||||||| |||||||||||| | ||||| |||||||| || ||||||||||| || |||||||| ||||||||||||||||||||||     | |     | || |||||  ||| | ||       | ||| ||    || ||||||||||   |||  || |||||
TAATAACTACATCTCCGTTGGTGCCTCTGGAGCTTTGTTTGGCTTACTTGGGTCTATGCTCTCCGAGCTTATTATGAACTGGACTATTTATTCCAACAAGgtcagcagaacagagactgtacctatattgttt-actccaatt-------cagttgttccctgc-aagtttcagtttgttcactcttgcag

upper sequence: GRMZM2G157384_T01 (Zea mays), 5'ss of exon 3
lower sequence: GLYMA16G32150.1 (Glycine max), 5'ss of exon 3

CAGTAACTACGTCTCTGTTGGTGCCTCTGGGGCTTTGTTTGGCCTCCTTGGATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaaagtgtattacgtgtgtactgttt-tgctc--tagtttttctct---------ctgtt--ttttttggctaagtttcagtcaattcgttcctgcag
 || ||| || | ||||||||||| ||||| ||| | ||||| || |||||| | ||||||||||| ||||| | |||||||| ||| ||| | || |||||     |      |  ||  | |||| | | | || |   ||||| || |            | ||  | || ||   |  |||     ||||| |   |    
TAGAAACAACATTTCTGTTGGTGCTTCTGGTGCTCTTTTTGGACTTCTTGGAGCAATGCTTTCAGAACTTATCACAAATTGGAGTATTTATACTAATAAGgt-gttggttcccatcctatttttgtattctgtgtgtttgttagttctttttaaaaggaaaattattaatgttatgaaaagattttgacaaattcctgtat----

upper sequence: GRMZM2G157384_T01 (Zea mays), 5'ss of exon 3
lower sequence: Vv02s0025g04130.t01 (Vitis vinifera), 5'ss of exon 3

-CAGTAACTACGTCTCTGTTGGTGCCTCTGGGGCTTTGTTTGGCCTCCTTGGATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtca--gcagaaagtgtattacgtgtgtactgttttgctctagtttttctctctgttttttttg-gctaagtttcagtcaattcgttcctgcag---------------------------------------------------------------------------------------
 ||  | | |  ||||||| ||||| ||||| ||| ||||||| || |||||| | |||||||||||||||||||  || |||| ||| ||| |||||||||| |  || |  | |   | |  |   |  | |||| || | || | | |   ||   |    | | |   ||||| |||| | ||| ||  |                                                                                        
TCAACA-CAATATCTCTGTGGGTGCGTCTGGTGCTCTGTTTGGACTTCTTGGAGCAATGCTTTCAGAGCTTATTACCAACTGGAGTATTTATACCAACAAGgtgactgctgctaatccttgatttacctttttttttccttttgtgtgtgtagttggggtgggggagatgtttttcactcaagttgttgctctaattattaatttgattttgaggcaggaagtttgaagaagattgtttagattcttggcatttaacctttcctcctttcttgcttttgtag

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|60342822|gb|DN209795.1|DN209795

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|78088538|gb|DV516931.1|DV516931

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|40335119|gb|CK369189.1|CK369189

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|88752104|gb|DY536245.1|DY536245

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|74241938|gb|DT649852.1|DT649852

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|149080701|gb|EE169761.2|EE169761

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCCACAAG                         GCAGCGGCAATCATAACTCTACTTTTTANTA-TTGTAATTAATCTGGCCAT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTA-TAATTGTAATTAATCTGGCCAT

EST: gi|76289252|gb|DV028820.1|DV028820

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|71446277|gb|DR827327.1|DR827327

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|22521141|gb|BU079952.1|BU079952

EST:     GATCTATGCTTTCAGAGCTTATTATGAACTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|148941580|gb|EC886517.2|EC886517

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|71762229|gb|DR960166.1|DR960166

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|87156908|gb|DY401697.1|DY401697

EST:     GATCTATGCTTTCAGAGCTTATTATGAACTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|74236231|gb|DT644145.1|DT644145

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|86468306|gb|DY234676.1|DY234676

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|78088539|gb|DV516932.1|DV516932

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|76289251|gb|DV028819.1|DV028819

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|148941581|gb|EC886518.2|EC886518

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|71448535|gb|DR829585.1|DR829585

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCCTT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|74241937|gb|DT649851.1|DT649851

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

EST: gi|71447543|gb|DR828593.1|DR828593

EST:     GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAG                         GCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT
genomic: GATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATT

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: 216

CAGTAACTACGTCTCTGTTGGTGCCTCTGGGGCTTTGTTTGGCCTCCTTGGATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaa ... gttcctgcagGCAGCGGCAATCATAACTCTACTTTTTATAATTGTAATTAATCTGGCCATTGGGATATTACCTCATGCTGATAATTTTGCCCACATTGGTGGATTTGCTT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 272

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGTAACTACGTCTCTGTTGGTGCCTCTGGGGCTTTGTTTGGCCTCCTTGGATCTATGCTTTCAGAGCTTATTATAAATTGGACTATCTATTCCAACAAGgtcagcagaaagtgtattacgtgtgtactgttttgctctagtttttctctctgttttttttggctaagtttcagtcaattcgttcctgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT