ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCGGGAGCAACTAAAGCAGCTTGTTTCGTCCATTGTAAAACCAAAAATCGTGCAGGGTAGAACTCTAAATGGGAAGGACTTTGTGTCTTTCTTGCAGCAGgtaaaatacctaatgatgtgattgttgatatgtatctgatcagttaattattagtaacttctcctgtgtttcag

Basic information

species	Zea mays
transcript	GRMZM2G305254_T06
intron #	12
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G305254_T05 (Zea mays), 5'ss of exon 12
lower sequence: LOC_Os03g58240.1 (Oryza sativa), 5'ss of exon 13

GCGGGAGCAACTAAAGCAGCTTGTTTCGTCCATTGTAAAACCAAAAATCGTGCAGGGTAGAACTCTAAATGGGAAGGACTTTGTGTCTTTCTTGCAGCAGgtaaaatacctaatgatgtgattgttgatatgtatctgatcagtta----attattagtaacttctcctgtgtttcag
||||||  || | |||||| | ||| |||||||   || ||||||||| |||||||| | |||||||||||| ||||| ||||| |||||||||||||||||| ||  | ||  |   | ||| |||| || | ||| |||  |||    ||| ||| | ||||||| |||||| |||
GCGGGATGAATTGAAGCAGGTCGTTGCGTCCATCACAAGACCAAAAATTGTGCAGGGGAAAACTCTAAATGGAAAGGAATTTGTTTCTTTCTTGCAGCAGgtagaacccttaccgtcattattcttgacatctctctaatccattagattatttttattgacttctcttgtgttccag

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|18963438|gb|BM660435.1|BM660435

EST:     TGCAGGGTAGAACTCTAAATGGGAAGGACTTTGTGTCTTTCTTGCAGCAG                         ATTCTTGAGGCTTTGAATAAAGGCG
genomic: TGCAGGGTAGAACTCTAAATGGGAAGGACTTTGTGTCTTTCTTGCAGCAGgtaaaatacc ... tgtgtttcagATTCTTGAGGCTTTGAATAAAGGCG

EST: gi|20301383|gb|BQ164326.1|BQ164326

EST:     TGCAGGGTAGAACTCTAAATGGGAAGGAC-TTGTGTCTTTCTTGCAGCAG                         ATTCTTGAGGCTTTGAATAAAGGCGAAATTCCATCAACTGGATCTCTGGTT
genomic: TGCAGGGTAGAACTCTAAATGGGAAGGACTTTGTGTCTTTCTTGCAGCAGgtaaaatacc ... tgtgtttcagATTCTTGAGGCTTTGAATAAAGGCGAAATTCCATCAACTGGATCTCTGGTT

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), 39 (downstream exon)
Score: 116

GCGGGAGCAACTAAAGCAGCTTGTTTCGTCCATTGTAAAACCAAAAATCGTGCAGGGTAGAACTCTAAATGGGAAGGACTTTGTGTCTTTCTTGCAGCAGgtaaaatacc ... tgtgtttcagATTCTTGAGGCTTTGAATAAAGGCGAAATTCCATCAACTGGATCTCTGGTTGAAATTTTTAACAAAGCCATTCTTGATCGCTGTCTGAAGGTGTACAGGG

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 101

Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 92