ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaaagatgagtaactaatgcatgggtctgtatactttaggggctcggtattaataaaactatgcacttattcttaaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA

Basic information

species	Zea mays
transcript	GRMZM2G315726_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G315726_T02 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g49590.1 (Oryza sativa), 3'ss of exon 4

-------gtaaagatgagta-actaatgcatgggtctgtatactttag---------gggctc---ggtattaataaaact-atgcacttattcttaaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA
        || |  | |||    | ||  | ||   | ||||||||||         ||  ||     |||   |||| || ||||  || |||| ||||||||||||||||||||||| ||   | |||||| | ||||||||  |||| || ||| || |||| |||||||||||| ||||||||||||| || |||||||||
gtagatactacatgttagtgtgttcatatacggagttctatactttagcctttagggggattctataatatcgctaaagcttatgcgtttcttctaaaatttcagCTATGAAGTTGTTCCGATGTTGGACAAGAAGAAGCATAAGTTTGATGGTCCACTACACTATTATGTATTCAACTGTCTTCTCTTCTCCCTCCTTGTTCTA

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|37383937|gb|CF629011.1|CF629011

EST:     TTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGT-GNACGGGC
genomic: TTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTG-ACGGGC

EST: gi|211123441|gb|FL433091.1|FL433091

EST:     GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
genomic: GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC

EST: gi|78084141|gb|DV512534.1|DV512534

EST:     GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
genomic: GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC

EST: gi|84969762|gb|DV170504.2|DV170504

EST:     GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAG                         CTATGAAGTTGTTTTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC
genomic: GTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCC

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: 44 (upstream exon), 46 (downstream exon)
Score: 17

GCCATGAGTTGTTTGCAGATGTTTCATTTCTTGTTTTCGTCAGTTCTTGGGTACTCCTCCGCCTTATATATTATCCGTTCTGGATTCTCTGGAGCACGAGgtaaagatga ... taaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 485

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 427

Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 13

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtatactttaggggctcggtattaataaaactatgcacttattcttaaatttcagCTATGAAGTTGTTCTGACTCTAGACAAGGAAAAGCATAAAGTTGACGGGCCAATATACTACTATGTATTCAACAGTCTTCTCTTCTCTCTACTTGTTCTA