ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
cis-regulatory elements

Sequence

atgc intronic sequence ATGC exonic sequence

GTAAGCATGGCTCAGAAAATGGCAACTGTTGAGCGAGTAGAAGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaaccaaattcctattgttcttcctataggtttcttcttttgcacagtgacagggttttttgctttcttgcatttcttctgcatcgcttgcat...

Basic information

species	Zea mays
transcript	GRMZM2G133919_T01
intron #	7
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G133919_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 5'ss of exon 7

GTAAGCATGGCTCAGAAAATGGCAACTGTTGAGCGAGTAGAAGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaaccaaattcct-attgttcttcctataggtttcttcttttgcaca-gtgacagggttttttgctttcttgcatttcttctgcatcgcttgcat----------------------------------------------------------------------------
|||||||||||||||||||||||||||||||| || |||||||||||||| ||||| || |||||||| ||||||||||||||||| |||||||   |||| ||||||  | | | |  |   | ||  | |||| | ||    | ||  ||    | |||| |||| | |||  ||     |  |   |||                                                                             
GTAAGCATGGCTCAGAAAATGGCAACTGTTGACCGTGTAGAAGAGCTTCTTGAGAAACTCCGTGCTGCCTCCTGGGATCATGCTGTTAAAGgta--gccaatcaaattattgagtatcttctttgtatttctcttgtgttatttatgtatca----tctttgttttcatacatacctgtcttagtgtgagcaaatttttgtggcatattctataaggagtaggcatcttttgaggttcgaatatcttagctgttggtttctgtgtgcag

upper sequence: GRMZM2G133919_T01 (Zea mays), 5'ss of exon 7
lower sequence: AT5G65620.1 (Arabidopsis thaliana), 5'ss of exon 7

GTAAGCATGGCTCAGAAAATGGCAACTGTTGAGCGAGTAGAAGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgta-caaccaaccaaattcctattgttcttcctataggtttcttcttttgcacagtgacagggttttttgctttcttgcatttcttctgcatcgcttgcat------------------------------------------------------
||||||||||||  ||||||||| |||||||||  || || ||||||| | |||||||| |||  ||| |||||||||   |||||  |||||| ||  |    | |       |||  |||  ||   ||| || |||   | |      || |  | |     ||||      |     || || ||                                                         
GTAAGCATGGCTATGAAAATGGCTACTGTTGAGAAAGCAGCAGAGCTTTTAGAGAAGCTTCGTAGTGCATCCTGGGATGCGGCTGTTCAAGgtaacatactgatacagagaagatgta-ttcaaatcaatttgttatttgttaaacaagttggctactgttgaaacttgttacggtcagaaatagcatgaggcattgggctatccaatacggaactttgactttcttgaatcgttgtataaattag

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|211206210|gb|FL245889.1|FL245889

EST:     AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAG                         ATATGGAAGATCTAAAAGTYCTTTGCGAAAGATTCTGGTTCTCCTGAAGCT
genomic: AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaa ... gtgtattcagATATGGAAGATCTGAAAGT-CTTTGCGAAAGATTCTGGTTCTCCTGAAGCT

EST: gi|32794079|gb|CD946315.1|CD946315

EST:     AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAG                         ATATGGAAGATC
genomic: AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaa ... gtgtattcagATATGGAAGATC

EST: gi|67011759|gb|CO440508.1|CO440508

EST:     AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAG                         ATATGGAAGATCTGAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTA
genomic: AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaa ... gtgtattcagATATGGAAGATCTGAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTA

EST: gi|67026706|gb|CO455455.1|CO455455

EST:     AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAG                         ATATGGAAGATCTGAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTA
genomic: AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaa ... gtgtattcagATATGGAAGATCTGAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTA

EST: gi|211206209|gb|FL245888.1|FL245888

EST:     AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAG                         ATATGGAAGATCTAAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTA
genomic: AGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaa ... gtgtattcagATATGGAAGATCTGAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTA

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: 47 (upstream exon), 49 (downstream exon)
Score: 208

GTAAGCATGGCTCAGAAAATGGCAACTGTTGAGCGAGTAGAAGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaa ... gtgtattcagATATGGAAGATCTGAAAGTCTTTGCGAAAGATTCTGGTTCTCCTGAAGCTAATGATTTGACTCACTGGGACCTTACCTTCTGGAGTGAACGACTGAGAGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 230

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 177

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 188

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTAAGCATGGCTCAGAAAATGGCAACTGTTGAGCGAGTAGAAGAGCTTCTCGAGAAGCTGCGTGCTGCTTCCTGGGATCATGCTGTCAAAGgtacaaccaaccaaattcctattgttcttcctataggtttcttcttttgcacagtgacagggttttttgctttcttgcatttcttctgcatcgcttgcat

- - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  ATGCTG