ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GAACACTCTTTCCGTTGCTCTTGTTGACACCTCAAAACCTGGGACTACTGATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGGgtaacaaagctgtattttacatgtcaaatttatgtttctctgctgaagcaacaccccagattttacttagcactttctttaagcacaaaatatgttttgctgaggagatggcattcatgagcag

Basic information

species	Zea mays
transcript	GRMZM5G873287_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G873287_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os01g39310.1 (Oryza sativa), 5'ss of exon 19

GAACACTCTTTCCGTTGCTCTTGTTGACACCTCAAAACCTGGGACTACTGATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGGgtaacaaagctgtattttacatgtcaaat--ttatgtttctctgctgaagcaacaccccagattt-tacttagca----ctttctttaagcacaaa--atatgttttgctgaggagatggcatt--catgagcag
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GAACACCCTGTCCCTTGCTCTAGTTGACACAGCAAGGCCAGGGACTACAGATAGGAGCATCCAATCGTTCGATCCACTTGCCTCTAGCTCATGGGAAAGGgtaaggaagctgtgtgctatgtttaatgctgtcatttttgtctgcccaagcgaccctttgtttttatccttatcagtaacttcttttcagcatgaaccatatgttttgctaagtaaatgtcatttgcacaagcag

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|78179393|gb|DV549766.1|DV549766

EST:     ATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGG                         GTTGCCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAGTTTGTGG
genomic: ATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGGgtaacaaagc ... tcatgagcagGTTGGCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGG

EST: gi|29130328|gb|CB381032.1|CB381032

EST:     ATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGG                         GTTGGCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGG
genomic: ATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGGgtaacaaagc ... tcatgagcagGTTGGCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGG

EST: gi|6859862|gb|AW355856.1|AW355856

EST:     ATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGG                         GTTGCCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAGTTTGTGG
genomic: ATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGGgtaacaaagc ... tcatgagcagGTTGGCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGG

EST: gi|60397891|gb|DN230707.1|DN230707

EST:     TCCAGTTCATGGGAAAGG                         GTTGCCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAGTTTGTGG
genomic: TCCAGTTCATGGGAAAGGgtaacaaagc ... tcatgagcagGTTGGCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGG

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: 441

GAACACTCTTTCCGTTGCTCTTGTTGACACCTCAAAACCTGGGACTACTGATAGGAGTATCCAATTGACCGATCCACTTGCCTCCAGTTCATGGGAAAGGgtaacaaagc ... tcatgagcagGTTGGCGAGGAGAAGACTTTAATTACCCCTGTGCAGTGCAAAAATTTGTGGAGGCAATTCAAGGCTGAAACTGAATATACAGTGACTCAAGCCTTAGCTG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 547

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 599