ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttcttgcctatgatatgttatgttgcttctgtgaagtgctgctttcgtagcttcttagcttgtgttgtgccttgtaatggaattacttgccttcactgatctgttttgtatttttatgtgtag

Basic information

species	Zea mays
transcript	GRMZM2G123732_T02
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G123732_T01 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g54920.1 (Oryza sativa), 5'ss of exon 5

GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttcttgccta-tgatatgttatgttgcttctgtgaag---tgctgctttcgtagcttct--tagcttgtgttgtgccttgtaatggaattacttgccttcactg---atctgttttgtatttttatgtgtag
||| || |||||||| |  ||||| |||||||| ||||||||||| || || |||||||||||| |||| ||||||||||||||||     |  ||  || | | | |  ||  | ||  |  |   |  || | | |||  ||    ||   |  ||     |||||  |   ||  |||  |||||      ||   |  |  || | |  ||||||
GTTGTACAATCTCACCAGTGTATGTTATCATTCTCTTTACCTTCCACTTCTCTATGTGACTTTCCTAGCAGACTTTTTCCAGgtactagggtatcttctgttctatcaacttattactacgctgctttcttgatcttgtacattgggatattctacgtaccctcttgttcttatatagcttttcttcatcaaaaattgctggttcatgtctgagtgtag

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|211324995|gb|FL127007.1|FL127007

EST:     GACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: GACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

EST: gi|211118164|gb|FL349423.1|FL349423

EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGGAAGACATGCTCCTA
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGG-AAGACATGCTCCTA

EST: gi|211474975|gb|FL438616.1|FL438616

EST:     CGCTTTACCTTCCCCTCCCATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

EST: gi|74244183|gb|DT652097.1|DT652097

EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

EST: gi|33092349|gb|CF052343.1|CF052343

EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

EST: gi|93011727|gb|EB637247.1|EB637247

EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

EST: gi|32933373|gb|CF038185.1|CF038185

EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

EST: gi|32934905|gb|CF039717.1|CF039717

EST:     CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAG                         GAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT
genomic: CGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCT

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), 43 (downstream exon)
Score: 80

GTTATATAATCTCACAATCGTATGCTATCATTCGCTTTACCTTCCCCTCCTATATGTGACTTTCTTAGCGGACTTTTTCCAGgtaccttctt ... ttatgtgtagGAGGAAGACATGCTCCTAGAGAGCGTTTACTATTCTGAAATGAAGGATGCTGGGTTCTTTGATGCTGACTGGGATTAATCGGTGGCTACTGCGCTCTATG

Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 60

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 72