ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAACCGCGACCATGTCACCGTCGCCACTGAGGACCTCGACGCCTTCGATGCCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTGgtgcgttggtttctcagagttttcgttatccgtctgtgctgtggatttcgtacttgactctcgtacatgggcctatgtag

Basic information

species	Zea mays
transcript	GRMZM2G450055_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G450055_T01 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g55410.1 (Oryza sativa), 5'ss of exon 2

CAACCGCGACCATGTCACCGTCGCCACTGAGGACCTCGACGCCTTCGATGCCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTGgtgcgt--tggtt-tctcagagttttcgttatccgtctgtgctgtggatttcgtacttgactctc---gtacatgggcctatgtag
||||||||||||||||||||||||||  |||||||||||||||||||| |||||||| || ||||||||||| ||||| || || ||||| || ||  ||||| ||  ||||| | || || |||| |||  |  |  || |||| ||| ||    ||   | |     |  | ||   | |||||
CAACCGCGACCATGTCACCGTCGCCATCGAGGACCTCGACGCCTTCGACGCCGAGCTGTCCGACAAGATCCGGAAGTCTCCCGCTGATTACCTACCGCTGgtgtgtgctggttctttctgaatttttgttggctctgggttctgttgatgtcaattttttgtgttaagatttagggttttgtgtag

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|211201211|gb|FL134396.1|FL134396

EST:     GAGCTCTCTGACNNAGATCCGCA-GTCGCCTGCCGATTATCTTCCCTTTG                         T-CGAGACGGCTGCGTCCGAAGTTCTCGCAAGCCTCCGTTCGAAAGTCGC
genomic: GAGCTCTCTGACA-AGATCCGCAAGTCGCCTGCCGATTATCTTCC-TTTGgtgcgttggt ... gcctatgtagTTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGC

EST: gi|91876627|gb|EB406584.1|EB406584

EST:     CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTG                         TTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC
genomic: CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTGgtgcgttggt ... gcctatgtagTTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC

EST: gi|149014583|gb|EE044230.2|EE044230

EST:     CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTG                         TTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC
genomic: CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTGgtgcgttggt ... gcctatgtagTTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC

EST: gi|78112949|gb|DV531343.1|DV531343

EST:     CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTG                         TTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC
genomic: CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTGgtgcgttggt ... gcctatgtagTTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC

EST: gi|149081132|gb|EE170239.2|EE170239

EST:     CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTG                         TTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC
genomic: CCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTGgtgcgttggt ... gcctatgtagTTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCC

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: 43 (upstream exon), 49 (downstream exon)
Score: 35

CAACCGCGACCATGTCACCGTCGCCACTGAGGACCTCGACGCCTTCGATGCCGAGCTCTCTGACAAGATCCGCAAGTCGCCTGCCGATTATCTTCCTTTGgtgcgttggt ... gcctatgtagTTCGAGACGGCTGCGTCCGAGGTTCTCGCAAGCCTCCGTTCGAAAGTCGCCGGCGAGACCGGGGAGATGGAGGAGCCAGTCCCAGGAGATGTCCAGATCT

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 18

Block sizes: 47 (upstream exon), 30 (downstream exon)
Score: 5