ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaacttctttattgaaccagtattttgtcattaaatttactctacttcagaaaacctgacctggaaaaaactgcagAGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTAAGCGGGAACCCTGGCCTAATGTTTCGGAAAATGCAAAAGATTTAGTTCG

Basic information

species	Zea mays
transcript	GRMZM2G311220_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G311220_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os01g61590.1 (Oryza sativa), 3'ss of exon 2

----gtaacttctttattgaaccagtattttgtcattaaatttactctacttcagaaaacctgacctggaaaaaactgcagAGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTAAGCGGGAACCCTGGCCTAATGTTTCGGAAAATGCAAAAGATTTAGTTCG
    ||  ||| | | || || |  |    | |||||   | |  ||| | ||| | || ||  |||||||     | |||||||||| ||||||||||| || || ||||||||||||||||||||||| || || ||||||||||| |||||||| |||||||| |||||||| |||||
gtatgttgcttttcttttaaaacctt-cgctatcattggctgtcatctccctcaaacaatctcgcctggaatttttt-cagAGACTGAGCAAGGGGTGGCACAAGCCATTCTTCGTGGAAATATCGATTTCAAACGCGAACCCTGGCCAAATGTTTCAGAAAATGCTAAAGATTTGGTTCG

upper sequence: GRMZM2G311220_T01 (Zea mays), 3'ss of exon 2
lower sequence: Vv08s0105g00390.t01 (Vitis vinifera), 3'ss of exon 2

--------------------gtaacttctttatt--gaaccagtattttgtcatt-----aaatttactctacttcagaaaacctgacctggaaaaaactgcagAGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTAAGCGGGAACCCTGGCCTAATGTTTCGGAAAATGCAAAAGATTTAGTTCG
                     ||  | |  | ||  || || || |||| | ||      ||||    ||   ||||   ||  |||  |    |    ||||||| ||||||||||||| || |||||||||||||||||    || ||||| ||  |||| || ||||| ||| |||| || | ||| ||   | |||||||
ggttgctttccttcctaatcctaggtgcaatgtttagagcctgtctttttttatctgtagaaatgctttccctttcatctaaagtgagtttttga----tgcagAGTCTGAACAAGGGGTTGCACAGGCTATTCTTCGTGGGCTAATAGATTTCAAAAGGGATCCATGGCCAAATATTTCAGAGAGTGCCAAGAGTCTAGTTCG

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|213178497|gb|FM182856.1|FM182856

EST:     AGGAGTTATCCTGTATATTTTATTATGTGGAGTCCCTCCATTTTGGGCAG                         AGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTA
genomic: GGGAGTTATCCTGTATATTTTATTATGTGGAGTCCCTCCATTTTGGGCTGgtaacttctt ... aaaactgcagAGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTA

EST: gi|78119680|gb|DV538064.1|DV538064

EST:     GGGAGTTATCCTGTATATTTTATTATGTGGAGTCCCTCCATTTTGGGCTG                         AGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTA
genomic: GGGAGTTATCCTGTATATTTTATTATGTGGAGTCCCTCCATTTTGGGCTGgtaacttctt ... aaaactgcagAGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTA

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), 48 (downstream exon)
Score: 177

CCTGAAGTATTGAAGAGAAACTATGGGCCAGAAATAGACATATGGAGTGCGGGAGTTATCCTGTATATTTTATTATGTGGAGTCCCTCCATTTTGGGCTGgtaacttctt ... aaaactgcagAGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTAAGCGGGAACCCTGGCCTAATGTTTCGGAAAATGCAAAAGATTTAGTTCG

Block sizes: 47 (upstream exon), 47 (downstream exon)
Score: 111

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 100

Block sizes: 43 (upstream exon), 48 (downstream exon)
Score: 102

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

attttgtcattaaatttactctacttcagaaaacctgacctggaaaaaactgcagAGACTGAACAAGGGGTGGCGCAGGCTATTCTTCGTGGAAATATCGATTTTAAGCGGGAACCCTGGCCTAATGTTTCGGAAAATGCAAAAGATTTAGTTCG