ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATTCCAACAACCTCAAGGACGCACTCAAGTACTCGGCGCAGATGCTCTCCGAACTGCGCACCTCGCGACTATCGCCGCACAAGTACTACGAGCTGTgtgagtaactgtggatttggagctgctgggtctgtggaattctggaagtgggatcggtcggaattctgatgggattcacttgtccgctgcag

Basic information

species	Zea mays
transcript	GRMZM5G825524_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G825524_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os03g58700.1 (Oryza sativa), 5'ss of exon 2

GATTCCAACAACCTCAAGGACGCACTCAAGTACTCGGCGCAGATGCTCTCCGAACTGCGCACCTCGCGACTATCGCCGCACAAGTACTACGAGCTGTgtgagtaactgt--ggatttggagctgctgggtctgtggaattctggaagtgggatcggtcggaattctgatgggattcacttgtcc-gctgcag
||||| |||||||||||||| || ||||||||||||||||||||||||||||| ||||| |||||||| || |||||||||||||| || || || |||||||   | |   |  |  |   | ||  ||  |   |||| |||  ||||  || |  || |||     ||| || | |  |   |||||||
GATTCGAACAACCTCAAGGATGCGCTCAAGTACTCGGCGCAGATGCTCTCCGAGCTGCGGACCTCGCGGCTCTCGCCGCACAAGTATTATGATCTATgtgagtgtttcttatgtgtcaggattcctcagtgcgcccaattttggctgtggtttcagctgggatttgatgggggtttattgattttgctgcag

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|211323478|gb|FL043268.1|FL043268

EST:     CTCCGAACTGCGCACCTCGCGACTATCGCCGCACAAGTACTACGAGCTGT                         ACATGAGGGCGTTTGATGAGATGAAGAAGCTGGAGATGTTCTTCAGGGAGG
genomic: CTCCGAACTGCGCACCTCGCGACTATCGCCGCACAAGTACTACGAGCTGTgtgagtaact ... tccgctgcagACATGAGGGCGTTTGATGAGATGAAGAAGCTGGAGATGTTCTTCAGGGAGG

EST: gi|18659312|gb|BM500271.1|BM500271

EST:     CTCCGAACTGCGCACCTCGCGACTATCGCCGCACAAGTACTACGAGCTGT                         ACATGAGGGCGTTTGATGAGATGAAGAAGCTGGAGATGTTCTTCAGGGAGG
genomic: CTCCGAACTGCGCACCTCGCGACTATCGCCGCACAAGTACTACGAGCTGTgtgagtaact ... tccgctgcagACATGAGGGCGTTTGATGAGATGAAGAAGCTGGAGATGTTCTTCAGGGAGG

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), 48 (downstream exon)
Score: 114

GATTCCAACAACCTCAAGGACGCACTCAAGTACTCGGCGCAGATGCTCTCCGAACTGCGCACCTCGCGACTATCGCCGCACAAGTACTACGAGCTGTgtgagtaact ... tccgctgcagACATGAGGGCGTTTGATGAGATGAAGAAGCTGGAGATGTTCTTCAGGGAGGAGACTCGCCGGGGCAGCTGCTCTGTGGTTGATATGTACGAGCTTGTGCA

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 106

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 86