ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagttataatcactttccttactatgtgcttggaaattgaaacatcttgctttactgggtgttcagagaaaatcaagaattgctgaatcgagtttcctgtattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATGATTTTCTTCCAGGATTACGCCGAGTGTGTTCTATGGAGTTTGGACAACA

Basic information

species	Zea mays
transcript	GRMZM2G048067_T03
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G048067_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os12g01922.1 (Oryza sativa), 3'ss of exon 15

gtaagtta-taatcactttccttactatgtgcttggaaattga--aacatcttgctt-tactgggtgttcag--agaaaatcaagaattgctgaatcgagtt--tcctgtattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATGATTTTCTTCCAGGATTACGCCGAGTGTGTTCTATGGAGTTTGGACAACA
||| |||| ||||  || ||||| | | |||||||||   ||     | | |||| |  |||   |  |      |    | ||  |||  |||||  || |  | |  ||||||| ||||||   || | |    |||||||| ||||||||||| || ||||||||||| |  ||  ||||||| ||||||||||| || ||||||||  ||| |||
gtaggttaataatttctatccttgccaagtgcttggaggatgcctgcctttttgcatgcactacattattgtgtggggtgtaaatgattattgaattcagctctttcaatattttgtagGAAATTTCTCGGTGGCCTTTAGGACTCCTCCTGTTAGTCCCCCTCAGCATGACTACCTCACAGGATTGCGCCGAGTGTGCTCGATGGAGTTCAGACCACA

upper sequence: GRMZM2G048067_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os11g01872.1 (Oryza sativa), 3'ss of exon 14

gtaagtta-taatcactttccttactatgtgcttggaaattga--aacatcttgctt-tactgggtgttcag--agaaaatcaagaattgctgaatcgagtt--tcctgtattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATGATTTTCTTCCAGGATTACGCCGAGTGTGTTCTATGGAGTTTGGACAACA
||| |||| ||||  || ||||| | | |||||||||   ||     | | |||| |  |||   |  |      |    | ||  |||  |||||  || |  | |  ||||||| ||||||   || |||    |||||||| ||||||||||| || ||||||||||| |  ||  ||||||| ||||||||||| || ||||||||  ||| |||
gtaggttaataatttctatccttgccaagtgcttggaggatgcctgcctttttgcatgcactacattattgtgtggggtgtaaatgattattgaattcagctctttcaatattttgtagGAAATTTCTCGATGGCCTTTAGGACTCCTCCTGTTAGTCCCCCTCAGCATGACTACCTCACAGGATTGCGCCGAGTGTGCTCGATGGAGTTCAGACCACA

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|30087149|gb|CB885357.1|CB885357

EST:     GATATGAATTCTG                         GAAACAAC-TGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATG
genomic: GATATGAATTCTGgtaagttata ... tattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATG

EST: gi|28576038|gb|CB281930.1|CB281930

EST:     GATATGAATTCTG                         GAAACAAC-TGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATG
genomic: GATATGAATTCTGgtaagttata ... tattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATG

EST: gi|31558447|gb|CD527659.1|CD527659

EST:     ATATGAATTCTG                         GAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATG
genomic: ATATGAATTCTGgtaagttata ... tattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATG

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: 161

AAAAATACTAGATTTAATAGTGGAGGTGCACATCGGGGAGAGACATCTGCTTCAAACTTTGGAATGGCACGCTCTTCATCCTGGCTTGATATGAATTCTGgtaagttata ... tattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATGATTTTCTTCCAGGATTACGCCGAGTGTGTTCTATGGAGTTTGGACAACA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 109

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 87

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 83

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctgggtgttcagagaaaatcaagaattgctgaatcgagtttcctgtattttgcagGAAACAACTTGATAAAATTTAGGACCCCTCCTGTTAGCCCTCCTCAGCATGATTTTCTTCCAGGATTACGCCGAGTGTGTTCTATGGAGTTTGGACAACA