ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCTGACAACAAAAATTGCGCCAGCAACACTTGGAGAAAGGGAGACATTTTTACCACGTGCTCCCAACTTGGATAACCGCGCTAGTGCTCTCCTGCAAAAGgtacctctttctaactggaggtgaacctctggtttattttaaaatgtacatgggatcagtttactttctggacattgttcaattcttggtttccagtgtg...

Basic information

species	Zea mays
transcript	GRMZM2G141258_T01
intron #	29
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G141258_T01 (Zea mays), 5'ss of exon 29
lower sequence: LOC_Os07g46590.1 (Oryza sativa), 5'ss of exon 16

CCTGACAACAAAAATTGCGCCAGCAACACTTGGAGAAAGGGAGACATTTTTACCACGTGCTCCCAACTTGGATAACCGCGCTAGTGCTCTCCTGCAAAAGgtacctctttctaactggaggtgaacctctggtttattttaaaatgtacatgggatcagtttactttctggacattgttcaattcttggttt--ccagtgtg
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CTTGACAGCGAAAATTGCACCAGCAACCCTTGGTGAACGAGAGACGTTTTTACCGCGTGCACCGAACTTGGATAATCGTGCTAGTGCTCTTCTACAAAAGgtaatc--tgcatgtcgcaccccctccccctacccctcccccaccctacttgctctatcttaagcttacacttacaactgtacctagagtttgcttattgtg

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|31628297|gb|CD526539.1|CD526539

EST:     TACCACGTGCTCCCAACTTGGATAACCGCGCTAGTGCTCTCCTGCAAAAG                         GAGTATGCTAAGTTTAGCGGTAAGAGCTTAAAAGTCAAAGGAAACACCCGC
genomic: TACCACGTGCTCCCAACTTGGATAACCGCGCTAGTGCTCTCCTGCAAAAGgtacctcttt ... atttgtcaagGAGTATGCTAAGTTTAGCGGTAAGAGCTTAAAAGTCAAAGGAAACACCCGC

EST: gi|61119137|gb|DN560098.1|DN560098

EST:     TACCACGTGCTCCCAACTTGGATAACCGCGCTAGTGCTCTCCTGCAAAAG                         GAGTATGCTAAGTTTAGCGGTAAGAGCTTAAAAGTCAAAGGAAACACCCGC
genomic: TACCACGTGCTCCCAACTTGGATAACCGCGCTAGTGCTCTCCTGCAAAAGgtacctcttt ... atttgtcaagGAGTATGCTAAGTTTAGCGGTAAGAGCTTAAAAGTCAAAGGAAACACCCGC

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: 48 (upstream exon), 46 (downstream exon)
Score: 128

CCTGACAACAAAAATTGCGCCAGCAACACTTGGAGAAAGGGAGACATTTTTACCACGTGCTCCCAACTTGGATAACCGCGCTAGTGCTCTCCTGCAAAAGgtacctcttt ... atttgtcaagGAGTATGCTAAGTTTAGCGGTAAGAGCTTAAAAGTCAAAGGAAACACCCGCCAGACAGTCAATAACGACAGTAATAGTGGAGTTCGATCAATGAGGGGCC

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 127

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 94