ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TACTGAGGTTGCAAAAGCCCGTGCGAGTACAAACAAAGTTGTTTGTTGCCATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgccaagatgaaacgaatttgcctttacgcgataaagaaatttcatgctacatgtttctttttcag

Basic information

species	Zea mays
transcript	GRMZM2G361398_T01
intron #	14
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G361398_T02 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os01g42270.1 (Oryza sativa), 5'ss of exon 13

TACTGAGGTTGCAAAAGCCCGTGCGAGTACAAACAAAGTTGTTTGTTGCCATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgccaagatgaaacgaatttgcctttacgcgataaagaaat---ttcatgctacatgtttctttttcag
||  |||||||||||||| ||||| ||||||||||| |||| |||||| |||||||| | ||||||||||||||| ||||| ||||| ||||||||||| ||||| |    |||     | | ||||     | |   | || |  ||   || || ||  || ||| ||||||||
TATCGAGGTTGCAAAAGCTCGTGCAAGTACAAACAAGGTTGATTGTTGTCATTTCTCGTCGGATGGGAAACTTCTAGCCACGGGAGGCCATGATAAAAAAgtgtgtaa---aagcaactatggattttgtggtgc-taaaaaggctatatatttatact-tatctttttttttcag

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|211173099|gb|FL062288.1|FL062288

EST:     TTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAG                         GTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG
genomic: TTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgc ... tctttttcagGTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG

EST: gi|21760046|gb|BQ635587.1|BQ635587

EST:     ATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAG                         GTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG
genomic: ATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgc ... tctttttcagGTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG

EST: gi|211173100|gb|FL062289.1|FL062289

EST:     TTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAG                         GTCGTTTTATGGTTTACAGATGTGTTAAAACGTAAATCCGCATTAGAAGAG
genomic: TTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgc ... tctttttcagGTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG

EST: gi|51593024|gb|CV072170.1|CV072170

EST:     ATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAG                         GTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG
genomic: ATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgc ... tctttttcagGTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG

EST: gi|211173101|gb|FL062290.1|FL062290

EST:     TTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAG                         GTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG
genomic: TTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgc ... tctttttcagGTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG

EST: gi|31358706|gb|CD443063.1|CD443063

EST:     ATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAG                         GTCGTTTGATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG
genomic: ATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgc ... tctttttcagGTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAG

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: 126

TACTGAGGTTGCAAAAGCCCGTGCGAGTACAAACAAAGTTGTTTGTTGCCATTTCTCATTGGATGGGAAACTTCTTGCCACCGGAGGGCATGATAAAAAGgtgtggatgc ... tctttttcagGTCGTTTTATGGTTTACAGATGTGCTAAAACGTAAATCCGCATTAGAAGAGCACTCTTCCCTAATTACAGATGTCCGATTCAGCCCTGGCATGACCCGCC

Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 24

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 22