ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtatgtgttttatcctgttttgcgttttttgtccgtcttgaattgtctctttgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGACATGGGGCATTCAAGGGCACCCGTCGTGCGTTCGTAAACAG

Basic information

species	Selaginella moellendorffii
transcript	EFJ12166
intron #	5
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: EFJ12166 (Selaginella moellendorffii), 3'ss of exon 5
lower sequence: AT4G10430.3 (Arabidopsis thaliana), 3'ss of exon 5

---------------------------------------gtatgtg-ttttatcctgttttgcgttttttgtccgtcttgaattgtctctttgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGACATGGGGCATTCAAGGGCACCCGTCGTGCGTTCGTAAACAG
                                       ||  |   | || || |   ||| | |   | |      ||||     | |  |||  |||||||| ||||||||||||||| |||||||| ||  || ||||| ||  | |||||||  ||  |||| || ||    || || |  ||||||
ttatctggattgacttaggtgttttgtttggctttttttgttcgaaatattctcataagttggggtgactttaacctctgaacctgatgtgggtc-ttcagGTGGCTATATCATCATTATTGTGCCATGGCTATGGCCCTTGTCAGCCTCACATGGGAAATCAAAGGTCAACCAAACTGTGTCCAGAAACAG

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|169064282|gb|FE471845.1|FE471845

EST:     GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGCGACATACGTCCATG                         GTGGGTATATC
genomic: GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGTGACATACGTCCATGgtatgtgttt ... tgtcgctcagGTGGGTATATC

EST: gi|70669921|gb|DN838498.1|DN838498

EST:     CACTGCGAGAAAACATTCTTCGAGTGAACGGAAGCGACCATACTTCCATG                         GGGGGTATATCACCATTTATTTTGCCATGGGTACTGCTCTTGGGAGTTTGA
genomic: CACTGCGAGAAAACATTCTTCGAGTGAACGGAAGTGAC-ATACGTCCATGgtatgtgttt ... tgtcgctcagGTGGGTATATCATCATT-ATTTTGCCATGGTTACAGCTCTTGTGAGTTTGA

EST: gi|169056974|gb|FE466201.1|FE466201

EST:     GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGCGACATACGTCCATG                         GTGGGTATATCACCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGAC
genomic: GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGTGACATACGTCCATGgtatgtgttt ... tgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGAC

EST: gi|169056973|gb|FE466200.1|FE466200

EST:     GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGCGACATACGTCCATG                         GTGGGTATATCACCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGAC
genomic: GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGTGACATACGTCCATGgtatgtgttt ... tgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGAC

EST: gi|169064281|gb|FE471844.1|FE471844

EST:     AGTGAACGGAAGCGACATACGTCCATG                         GTGGGTATATCACCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGAC
genomic: AGTGAACGGAAGTGACATACGTCCATGgtatgtgttt ... tgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGAC

EST: gi|169032393|gb|FE440950.1|FE440950

EST:     GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGCGACATACGTCCATG                         GTGGGTATATCACCATTATTTTGCCATGGTTACAGCTC
genomic: GCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGTGACATACGTCCATGgtatgtgttt ... tgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTC

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 1 RNA-Seqlibrary.

Block sizes: 33 (upstream exon), 34 (downstream exon)
Score: 3

GCATGGCTGCTGTTCTTCTACACCAGCTTGGCACTGCGAGAAAACATTCTTCGAGTGAACGGAAGTGACATACGTCCATGgtatgtgttt ... tgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGACATGGGGCATTCAAGGGCACCCGTCGTGCGTTCGTAAACAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gttttatcctgttttgcgttttttgtccgtcttgaattgtctctttgtcgctcagGTGGGTATATCATCATTATTTTGCCATGGTTACAGCTCTTGTGAGTTTGACATGGGGCATTCAAGGGCACCCGTCGTGCGTTCGTAAACAG