ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGTCTCCAGGAGCACCTGTTCCAGAAAATACCCCTTGTTCAGAAGATTCAGGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaatatatcgccgttttggctttgaactggtctaccaatgccagatgttcttcagattcaagtgccttcatgtccagagaatgctcatacttagattatatgcag

Basic information

species	Zea mays
transcript	GRMZM2G017616_T02
intron #	4
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G017616_T02 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g08220.1 (Oryza sativa), 5'ss of exon 4

GGTCTCCAGGAGCACCTGTTCCAGAAAATACCCCTTGTTCAGAAGATTCAGGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaatatatcg---ccgttttggctttgaactggtctaccaatgccagatgtt-cttcagattcaagtgccttcatgtccagagaatgctcatacttagattata-tgcag
|| || || || ||||| |||||||| ||||| ||||||||||||||||| || || || || ||||||||||| || || || ||||| |||||||| |||||| ||     ||     |  ||||  | |  | ||| | | |||     | | ||| ||||  |||||||  || | | |       | |    ||   |   | ||  |||||
GGCCTGCAAGAACACCTATTCCAGAAGATACCACTTGTTCAGAAGATTCAAGAGTCGAGCGAAGGGATGCTTCGTTACGACACTCCTAGCATTCTTTCTAgtaagcaatgatcattaattcgttttttacctcaagctgatttgccagcagaaaaagtttcttcgaattcaagaacccttaagaatcaccactaacaatgtctccctcattctgcag

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|211506486|gb|FL158295.1|FL158295

EST:     GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCA                         AGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG
genomic: GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaa ... ttatatgcagAGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG

EST: gi|211506485|gb|FL158294.1|FL158294

EST:     GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCA                         AGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG
genomic: GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaa ... ttatatgcagAGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG

EST: gi|71315075|gb|DR794165.1|DR794165

EST:     GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCA                         AGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG
genomic: GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaa ... ttatatgcagAGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG

EST: gi|211506487|gb|FL158296.1|FL158296

EST:     GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCA                         AGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGATTGACTGTGG
genomic: GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaa ... ttatatgcagAGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG

EST: gi|78103541|gb|DV521969.1|DV521969

EST:     GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCA                         AGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG
genomic: GGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaa ... ttatatgcagAGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGG

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: 42 (upstream exon), 49 (downstream exon)
Score: 83

GGTCTCCAGGAGCACCTGTTCCAGAAAATACCCCTTGTTCAGAAGATTCAGGAATCAAGTGAGGGGATGCTTCGCTATGATACACCTAGAATTCTTTCCAgtaagtaaaa ... ttatatgcagAGGACAAGTTTGCATGGCTCCGTGACGATGAGTTTGCTCGACAGACTGTGGCAGGAATAAACCCAGTTAGCATCACCAGGCTCACG

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 111

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156