ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CCCTCGACCTCGATGTGCTGCAGATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAGgtaggcacccatctcgaatcaatctgttgacggacgatctgttggtttcacttttcaccgaccccttgtttgtctggtgatgccttcttcaag

Basic information

species	Zea mays
transcript	GRMZM2G042552_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G042552_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g01810.1 (Oryza sativa), 5'ss of exon 2

CCCTCGACCTCGATGTGCTGCAGATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAGgtaggcacccatctcgaatcaatctgttgacggacgatctgttggtttcacttttcaccgaccccttgtttgtctggtgatgccttcttcaag
                       |||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||| ||||| |||||||||  |   |   || |  || ||  ||      ||||        ||  |  ||  | ||  |    || ||   ||   |  ||  |||  
-----------------------ATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGTCCATCAGGGAGGCCGCCAAGCGCAACGACATCGGATCGGCCAAGgtacccctacgcttccatccattcgatt------cgattccacttgtttgcggtttgctgatgcgc-attcgt---gttgggttttggtcag-

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|166458771|gb|EG039295.1|EG039295

EST:     AGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAG                         GCGCTGGCCAAGGAGGTGG
genomic: AGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAGgtaggcaccc ... cttcttcaagGCGCTGGCCATGGAGGTGG

EST: gi|32834245|gb|CD973923.1|CD973923

EST:     GCGCAACGACATGGGATCCGCCAAG                         GCGCTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTAC
genomic: GCGCAACGACATGGGATCCGCCAAGgtaggcaccc ... cttcttcaagGCGCTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTAC

EST: gi|113702321|gb|EE679825.1|EE679825

EST:     AGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAG                         GCGCTGGCCAAGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTAC
genomic: AGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAGgtaggcaccc ... cttcttcaagGCGCTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTAC

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), 46 (downstream exon)
Score: 123

CCCTCGACCTCGATGTGCTGCAGATGTGCAGAGGGAGGAGAAGAAGGTGGAGAAGGCCATCAGGGAGGCCGCCAAGCGCAACGACATGGGATCCGCCAAGgtaggcaccc ... cttcttcaagGCGCTGGCCATGGAGGTGGTGCGCTCGAGGAAGGCAGTCAACCGCCTGTACGAGAACAAGGCCCAGCTCAACTCCATCTCCATGCACCTTGGCGAAATCG

Block sizes: 49 (upstream exon), 46 (downstream exon)
Score: 170

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 152