ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATTACAATACGTGAAATCCGTGAACATGTGTGGTTCAAGATCCGACTTCCGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgtataattttattgtgtgcgtatcaacttggcgacgtgtatttgtttccttcagacttaagaatcccctgcttttatggatgacactattccgtaaaatactttgtcttttctacttcaggagatgatttgaaattgttttgaattttgtag

Basic information

species	Zea mays
transcript	GRMZM2G077278_T01
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G077278_T01 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os05g45420.3 (Oryza sativa), 5'ss of exon 6

GATTACAATACGTGAAATCCGTGAACATGTGTGGTTCAAGATCCGACTTCCGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgt---ataattttattgtgtgcgtatcaacttggcgacgtgtatttgtttccttcagacttaagaatcccctgcttttatggatgacactattccgtaaaatactttgtcttttctacttcaggagatgatttgaaattgttttgaattttgtag
||| || |||||||||||||||||||||  ||||||||   |  | |||||||| ||||| |||||||| ||||| |||||||| ||||| |||||||||||   ||  |   ||| ||    || | | ||   | ||| | | || ||  || | ||||          || ||| ||  |||  |   ||  |||                                                         
GATCACCATACGTGAAATCCGTGAACATCAGTGGTTCACAGTTGGTCTTCCGCGTTATTTAGCTGTGCCACCTCCTGACACTGCACAACAGGTTAAAAAGgtaacatgctgccattatgcatctaactatttaaagccgtat-tctgctt--ttgaaactttcag--tgtttgatttgatcaatgtga--gttttgtag--------------------------------------------------------

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|76934830|gb|DV174040.1|DV174040

EST:     CAAGTTAAAAAG                         GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT
genomic: CAAGTTAAAAAGgtataatttt ... aattttgtagGTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT

EST: gi|76933421|gb|DV173441.1|DV173441

EST:     CAAGTTAAAAAG                         GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT
genomic: CAAGTTAAAAAGgtataatttt ... aattttgtagGTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT

EST: gi|15312951|gb|BI478479.1|BI478479

EST:     CTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAG                         GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT
genomic: CTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgtataatttt ... aattttgtagGTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT

EST: gi|67028292|gb|CO457041.1|CO457041

EST:     CACGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAG                         GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT
genomic: CGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgtataatttt ... aattttgtagGTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT

EST: gi|211429825|gb|FL327475.1|FL327475

EST:     CGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAG                         GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT
genomic: CGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgtataatttt ... aattttgtagGTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT

EST: gi|9254260|gb|BE344728.1|BE344728

EST:     CACGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAG                         GTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT
genomic: CGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgtataatttt ... aattttgtagGTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAAT

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: 144

GATTACAATACGTGAAATCCGTGAACATGTGTGGTTCAAGATCCGACTTCCGCGCTATTTGGCTGTGCCGCCTCCAGACACTGCTCAACAAGTTAAAAAGgtataatttt ... aattttgtagGTCGACGAGGAAACTCTTAATGATGTTATTAAGATGGGTTTTGACAAGAATCAGCTAATTGAATCTCTGCAAAACAGATTGCAGAATGAG

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 162

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 285