ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtacaagcgacactgaaacattttttgtttgtaagcaaaagatatggcaacattgtattgaactggcaatataataactttgatcagccaccagctaccttgaaaacatttgtttcaaatgcaaacatgattaatatgaaccttgcagATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTGGTTGAGCATCAGATTATGCTTGACCATAGCACTGGACGCTCACGTGGCTTTGGATTTGTCAC

Basic information

species	Zea mays
transcript	GRMZM2G064518_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G064518_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os06g37000.1 (Oryza sativa), 3'ss of exon 3

gta-caagcgacactgaaacattttttgtttgtaagcaaaagatatggcaacattgtattgaactggcaatataataactttgatcagccaccagctaccttgaaaacatttgtttcaaatgcaaacatgattaatatgaaccttgcagATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTGGTTGAGCATCAGATTATGCTTGACCATAGCACTGGACGCTCACGTGGCTTTGGATTTGTCAC
||| | |||   ||| |    |||  | |||  |||||||| ||||       |||||||   || | || | |||  |||  ||            ||  | || |   || | ||      ||| ||||||   ||||| ||| |||||||||| |||||||| ||||| || ||||||||||| |||||||||||||| |||||||||||| ||||||| || ||||| |||||||| ||||||||
gtagccagcagaactaagttgtttcctttttacaagcaaaa-atatat-----ttgtatt---ctagaaa-acaatggcttgaat------------actctaaataatgttatgtcttg-ataaatatgattgtcatgaaacttccagATAAATTGAAGGAGCATTTCTCTTCATATGGGAAGGTAGTTGAGCATCAGATAATGCTTGACCATGGCACTGGGCGGTCACGAGGCTTTGGCTTTGTCAC

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|13198506|gb|BG354355.1|BG354355

EST:     TAAGACAAAAAAGATCTTTGTGGGTGGTATTCCACCATCTCTTACCGAAG                         ATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTG
genomic: TAAGACAAAAAAGATCTTTGTGGGTGGTATTCCACCATCTCTTACCGAAGgtacaagcga ... aaccttgcagATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTG

EST: gi|211210055|gb|FL412302.1|FL412302

EST:     TAAGACAAAAAAGATCTTTGTGGGTGGTATTCCACCATCTCTTACCGAAG                         ATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTGGTTGAGCATCAGA
genomic: TAAGACAAAAAAGATCTTTGTGGGTGGTATTCCACCATCTCTTACCGAAGgtacaagcga ... aaccttgcagATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTGGTTGAGCATCAGA

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), 41 (downstream exon)
Score: 725

GAAGTCAAAAGGACTGTTCCAAAAGAGGAAATGTCATCGAAAGACGGTCCTAAGACAAAAAAGATCTTTGTGGGTGGTATTCCACCATCTCTTACCGAAGgtacaagcga ... aaccttgcagATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTGGTTGAGCATCAGATTATGCTTGACCATAGCACTGGACGCTCACGTGGCTTTGGATTTGTCAC

Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 291

Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 183

Block sizes: 49 (upstream exon), 41 (downstream exon)
Score: 424

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gctaccttgaaaacatttgtttcaaatgcaaacatgattaatatgaaccttgcagATAAATTAAAGGAGCACTTCTCATCGTATGGGAAGGTGGTTGAGCATCAGATTATGCTTGACCATAGCACTGGACGCTCACGTGGCTTTGGATTTGTCAC