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

...ttttcattcagtgttcgctgcattctacattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA

Basic information

species	Zea mays
transcript	GRMZM5G840909_T02
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os03g61810.1 (Oryza sativa), 3'ss of exon 3

-----ttttcattcagtgttcgc------tgcattctacattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
     ||  ||  || | |  ||      ||||||  |||||||||| | || |||||||  |  |         || | ||  ||||  ||||| | || |||    |||||||||||||||||||| ||||||||| |||| || |||||||| |||||||| ||||| || |||||||||||||| || ||||| |||||||| ||||
attctttgccagccaatttgggccgataatgcatttaacattagttt-ctttccattgtttggtta---------tcttttcacataataaatgt-ttttctgtgctatagGCTTGCAAAAAGCTTGGAAAAATTGAGTTGTCAGACTGTGAAATGTATGCATCATGTGAACCTTGCCCAATGTGTTTCGGCGCTGTGCATCTATCACGGA

upper sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA13G17790.1 (Glycine max), 3'ss of exon 3

ttttcattcagtgttcgctgcat-tctacattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaacta--gGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
       ||  |||  |   ||| | | ||||| ||||  | |   |||||            | |        || |   ||| |   |||  |   ||  ||||||||| ||||||  | | || || ||  | ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||  | || || || || |
--aaatctcgctgtatgactcatgtgtgcatta-tttttttatagatgttataaactttatgcagtgtcaaaaaatgattcatgcagtgttttcattttacagGCTTGCAAGAAGCTTAAGCAGATAGAACTTGCTGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA

upper sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA17G04720.2 (Glycine max), 3'ss of exon 3

ttttcattcagtgttcgctgcattctacattagttttccttt-cattgttaaggcaagagaatactca-tctcttataaccaatgtatc--ttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
       ||| |||  |   |  | | | ||  |||| ||    ||  | ||    |   | |  | | |     || |   ||| |    |||  |  |  ||||||| || ||||||  | | || || ||  | ||||||||||| ||||| |||||||| || ||||| ||||| ||||||||  | || || || || |
----agctcattgtatgactctgtatgccttcttttttctagatataataaactttatgcagtgttaaataaaaaatgattcatgcagtgttttcatttaacagGCTTGTAAGAAGCTTAAGCAGATAGAACTTGCAGATTGTGAAATATATGCTTCTTGTGAACCTTGCCCCATGTGCTTTGGTGCAATCCACCTTTCTCGAA

upper sequence: GRMZM5G840909_T02 (Zea mays), 3'ss of exon 3
lower sequence: Vv14s0030g01610.t01 (Vitis vinifera), 3'ss of exon 3

ttttcattcagtgttcgctgcattctacattagttttcctttcattgttaaggcaagagaa--tactcatctcttataacc--aatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA
     |    ||| ||  || ||   | ||  |       |||| |  |      || ||   |  |  | ||| ||      |||| | | ||  |     |||| || || |||||     |||||||||| || || |||||||| ||||| ||||||||||| ||||||||||| ||||||||| | ||||| ||  | |
-aactagattgtgctcattgaatgacaaatctgcaagtgattcacttctcttttcagtgatactctttgtttctcatgcttggaatgaaaccttcctg---cagGCATGTAAGAAGCTCAATCAAATTGAGCTATCAGACTGTGAAATCTATGCCTCTTGTGAGCCTTGCCCAATGTGCTTTGGTGCTATACATCTTTCAAGAA

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|60340724|gb|DN207697.1|DN207697

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|74244654|gb|DT652568.1|DT652568

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|211533256|gb|FL397681.1|FL397681

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|211111076|gb|FL388624.1|FL388624

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|93012688|gb|EB638208.1|EB638208

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|211194115|gb|FL380863.1|FL380863

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|94474369|gb|EB703327.1|EB703327

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|89252884|gb|DY624670.1|DY624670

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|5361194|gb|AI795614.1|AI795614

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|211162917|gb|FL392799.1|FL392799

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTWACTGCGATAAGAGAG                         GCTTGCGAAAHGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

EST: gi|211377789|gb|FL432426.1|FL432426

EST:     TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAG                         GCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA
genomic: TGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCA

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: 71

AGTTGTTGTCCATAATGATGAAGTAATAGTTAGCTGCCATAACATGGTTTTGAAGAACACTGATCCAACTGCGCATGCTGAAGTAACTGCGATAAGAGAGgtaggatgct ... tgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 127

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 142

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 96

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

tgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA

                          ttataac  putative branch site (score: 96)
                                      tatctttt  putative PPT
                                          ttttgtaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttttcattcagtgttcgctgcattctacattagttttcctttcattgttaaggcaagagaatactcatctcttataaccaatgtatcttttgtaaactagGCTTGCAAAAAGCTTGGGAAAATTGAGCTGTCGGATTGTGAAATTTATGCATCTTGTGAGCCATGCCCAATGTGTTTTGGTGCTGTTCATCTATCCCGGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGTT
-tttcatt
- - cattcag
- - - - - - - - - tgcattc