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

gtatggcctgcactgcttgcttgcttgcttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAGCAAGGGGAAATCTTGGCGATGCAATATAATACTCA

Basic information

species	Zea mays
transcript	GRMZM2G126900_T03
intron #	3
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G126900_T03 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os06g36560.1 (Oryza sativa), 3'ss of exon 4

--gtatggcctgcactgcttgcttgcttg----------cttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAGCAAGGGGAAATCTTGGCGATGCAATATAATACTCA
     |     | | | || |  |    |             | || | || ||   |    | |        | |||  |       | || |||||||| |||||||||||||||||||| || ||||| ||||||||||| |||||| | |||||||                                        
caacctctttggaattactcggctaaaggaagaaagaaatgaaatggcaatacagtggggcacacttgtgacgtgtaacatgttctcttttctttttcagATCTGGGCAAGGTGCTGCTGCATCCCAGCTTTGGGGAGCTCCCACAGTGGTCAGTCGTCG----------------------------------------

upper sequence: GRMZM2G126900_T03 (Zea mays), 3'ss of exon 3
lower sequence: AT1G14520.1 (Arabidopsis thaliana), 3'ss of exon 4

gtatggcctgcactgcttgctt--gcttgcttac-tgccgatg-caactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAG-------CAAGGGGAAATCTTGGCGATGCAATATAATACTCA
   |    |  ||| | || ||  | ||| | || |    ||  |   |  ||     | | || | |  |     |   ||| | |  |||| || || || || || || ||| |    || || ||||||||||||||||||||||||||| |        ||  ||||  |  |   |||| ||| ||       
--gtaaattatactccctgattcggtttgatcacgttaaaatatcgtttaccggtttaatgattttgtgtttggtgtgtatgtgaat--cagATCTTGGAAAAGTTCTTCTTCACTCTTCATTTGGTGAGCTCCCTCAGTGGGCTGTCGTCGGTGATACATTTCCAGTGGGATGTGCTTTTGATG-AATCTAT------

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|148942392|gb|EC887411.2|EC887411

EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG

EST: gi|19821829|gb|BQ047853.1|BQ047853

EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGCGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG

EST: gi|18964769|gb|BM661199.1|BM661199

EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGCGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG

EST: gi|211533468|gb|FL294716.1|FL294716

EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGNGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG

EST: gi|211530472|gb|FL294712.1|FL294712

EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG

EST: gi|211533473|gb|FL294721.1|FL294721

EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGG

EST: gi|211530466|gb|FL294706.1|FL294706

EST:     AAGGACTACCCCGACGAGGACTGGCTCCACCTTCAC-GGACTCATTCACG                         AACTGGGCAAGGTGCTGCTGCACCCAAGGCTTCGGGGAGCTCCCTCAAGGG
genomic: AAGGACTACCCCGACGAGGACTGGCTCCACCT-CACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAG-CTTCGGGGAGCTCCCTCA-GTG

EST: gi|211530469|gb|FL294709.1|FL294709

EST:     CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACG                         ACCTGGGCAAGGTGCTGCTGC
genomic: CAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGC

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 3 RNA-Seq libraries.

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 518

CTGGACATGCCCCAGATCGAGCACCTGCTGCAGACCGCCGAGGCCATCCGCAAGGACTACCCCGACGAGGACTGGCTCCACCTCACCGGACTCATCCACGgtatggcctg ... tcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAGCAAGGGGAAATCTTGGCGATGCAATATAATACTCA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 245

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAGCAAGGGGAAATCTTGGCGATGCAATATAATACTCA

                                    aactcac  putative branch site (score: 277)
                                             tcattttc  putative PPT
                              taatctaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggcctgcactgcttgcttgcttgcttactgccgatgcaactgtcgtcgccacgcttctctaatctaactcactgtcattttcagACCTGGGCAAGGTGCTGCTGCACCCAAGCTTCGGGGAGCTCCCTCAGTGGGCTGTCGTCGGTAAGCAAGGGGAAATCTTGGCGATGCAATATAATACTCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG