ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GGATAGTGAATTTGATTTAGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttaccctctagtacttcccaaaacacacgtacatgtgcacacatgtagccaatgagagtgtttggtttattttattgccctttgtattatccct...

Basic information

species	Zea mays
transcript	GRMZM2G090722_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G090722_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g24354.1 (Oryza sativa), 5'ss of exon 2

GGATAGTGAATTTGATTTAGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttaccctctagtacttcccaaaacacacgtacatgtgcacacatgtagccaatgagagtgtt--tggtttattttattgccctttgtattatccct
 || |||||||||||||| |||||||||||||  ||||| |||| | |||| |||||||| |||||||| || || ||||| |||||||||||||||||||||  |||   | ||   || ||   | |||   |   || |    | || | |      |  |||||  ||   |||  || |     |   |||||    
AGACAGTGAATTTGATTTGGAGAATATTGTCACTGCTGCGAGAGTTGCTGGGAAGAAAGTCCCTGTTTTGCTCAGGATAAACCCAGATGTGGATCCACAGgtaaagtttttc-ctcccacctcaggatacagtgggggatttagttatat-tggtatgctattgtgttattgtcatataatactagaaatcagattatatag

upper sequence: GRMZM2G090722_T02 (Zea mays), 5'ss of exon 2
lower sequence: GLYMA19G36580.1 (Glycine max), 5'ss of exon 2

GGATAGTGAATTTGATTTAGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttaccctctagtacttcccaaaacacacgtacatgtgcacacatgt------agccaatgagagtgtttggtttattttattgccctttgtattatccct
 |||||||| ||||| || || || |||||    ||||||| |    |||| ||||| ||   |||||||||| | || ||||| |||||||||||||||||||| |      |  ||    | ||  |    || |  |   | ||   ||      |  || | ||||  |   |    ||||       |||| |  |     
TGATAGTGAGTTTGACTTGGAAAACATTGTAGAGGCTGCAAAAAGGGCTGGGAAGAAGGTCAATGTTTTACTTCGGATTAATCCTGATGTGGATCCACAGgtatgttgttgtacaggtttgacacacgagtagcgaagtttgactcatgcgtcttgtaattcacttagaggatagag---gttttggcaatttttgcaacaat---

upper sequence: GRMZM2G090722_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv09s0070g00580.t01 (Vitis vinifera), 5'ss of exon 2

GGATAGTGAATTTGATTTAGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatg-gttaccctctagtacttcccaaaacacacgtac----atgtgcacacatgtagccaatgagagtgtttggtttattttattgccctttgtattatccct
 ||||||||||||||||| || |||||| |   ||||||||||  | |||| ||||| ||   |||||||||||| || ||||||||||||||||| |||||||| | |  | |    || |||  |    ||   ||     ||||       |||    |      || |||   |||  ||       ||||  ||||    
TGATAGTGAATTTGATTTGGATAATATTATATCAGCTGCAAGAATTGCTGGCAAGAAGGTCAATGTTTTACTTAGGATCAATCCAGATGTGGATCCTCAGgtatgtgctgtcattgtttaattctaatgttacgaataatgtaatgttgtagggtgttcatagaacaggtatttcccttaggttgggtaaatttg-gttat----

upper sequence: GRMZM2G090722_T02 (Zea mays), 5'ss of exon 2
lower sequence: Vv03s0038g04490.t01 (Vitis vinifera), 5'ss of exon 2

GGATAGTGAATTTGATTTAGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatg----gttaccctctagtact--tcccaaaacacacgtacatgtgcacacatgtagccaatgagagtgtttggtttattttattgccctttgtattatccct
 ||||||||||||||||| || |||||| |   ||||||||||  | |||| ||||| ||   |||||||||||| || ||||||||||||||||| ||||||||    || ||  | || | ||  |   |  |   | ||| ||||       |||    |      || ||    |||  ||       ||||  ||||    
TGATAGTGAATTTGATTTGGATAATATTATATCAGCTGCAAGAATTGCTGGCAAGAAGGTCAATGTTTTACTTAGGATCAATCCAGATGTGGATCCTCAGgtatgtgctgtcactgtttaattctaatgttacgaataatgta-atgttgtagggtgttcatagaacaggtattgcccttaggttgggtaaatttg-gttat----

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|149009813|gb|EE041699.2|EE041699

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|148944671|gb|EC889806.2|EC889806

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|149085087|gb|EE174595.2|EE174595

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|9731558|gb|BE510310.1|BE510310

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|148964387|gb|EC905763.2|EC905763

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|76017251|gb|DT944421.1|DT944421

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|50331439|gb|CO526565.1|CO526565

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|148941210|gb|EC886099.2|EC886099

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|148982703|gb|EE028519.2|EE028519

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|149059656|gb|EE156999.2|EE156999

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

EST: gi|148940638|gb|EC885449.2|EC885449

EST:     GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAG                         GTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC
genomic: GAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGC

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: 257

GGATAGTGAATTTGATTTAGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttac ... tttccaacagGTACATCCATATGTTGCCACGGGAAATAAAACATCCAAATTCGGGATCCGCAATGAGAAATTGCAATGGTTTTTGAACTCTATCAAGTCATACTCGAATG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 183

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 169

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATAGTGAATTTGATTTAGAGAATATTGTCAGAGCTGCAAGAGCTACTGGAAAGAAAGTGCCTGTTTTACTTAGAATAAATCCAGATGTGGATCCACAGgtatggttaccctctagtacttcccaaaacacacgtacatgtgcacacatgtagccaatgagagtgtttggtttattttattgccctttgtattatccct

- - - - - - - - - - - - - - - - - - - - - - - - -  AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaacaca