ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtagtgttttattattacttacacacccgaattcactgtttgtgtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG

Basic information

species	Selaginella moellendorffii
transcript	EFJ28584
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9

--------------------------------------------gtagtgttttattattacttacacacccgaattcactgtttgt-gtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG
                                             |  ||| | |||   | |||   |    |||  | ||| | | || |||||    ||||||||  | ||||| || |  |||||  | ||||| || || || |||||||| |||||||| |||||||||||||| ||||| |||||| |||||| | 
tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttga---gcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA

upper sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: GLYMA02G43540.2 (Glycine max), 3'ss of exon 9

--------------------------------------------gtagtgttttattattacttacacacccgaattcactgtttgtgtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG
                                             |  ||| | |||   | ||||  | |  |||  | ||| | | || ||   |  ||||||||  | |||||||| |  |||||  | ||||| || || || |||||||| |||||||| || ||||||||||| ||||| |||||| |||||| | 
tttgcattttgcttagtcaaatttaaattttcttggcgtggtatctgttgtatgattgaaagttactgagctaaatgtaatgtgtcttttctt--tgagcagGTCAAAATTTGGTGCACTAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGTTGTGTCAAATATAATCCTGGATCTGGCAATTATA

upper sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 9

-------------------------------gtagtgttttattattacttacacacccgaattca---ctgttt--------gtgtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG
                                || || |||   ||     ||  |||  | ||     |||||          ||| | | |   |||||||||  | |||||||| |  |||||| | || || || |||||||||||||| ||||| || || |||||||| || ||||| |||||||||| || | 
agttcattataatcagggtactggggactccatattggtttgacatgctaaactaaccatagtttgtatctgttatgaacttaatgtatgtaataaacagGTCAAAGTTTGGTGCACAAACCAGGAGGCTAGCGTTCTTAACATTGACATGAAAGCAAATATATGTTGTGTCAAGTATAATCCTGGATCTAGCATTTATA

upper sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 9
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 9

-------------------------------------------------------------------------------------gtagtgttt--tattattacttacacacc-cgaattc--actgtttgtgt-ttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG
                                                                                     | ||| ||    || ||   | | |  |     || |  | ||||| | | ||        ||||| ||| | |||||||| ||||| ||| |||| ||  | || || |||||||||||||| ||||||||||| || || ||||| ||||| ||||  | ||
gtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttatttggagttttccgcatcatgtttaatatgcggttgatccgaaatgtttttatgttactgtttgcagGTGAAGATATGGTGCACGAGGCAAGAGTCAAGCGTGATAAATATAGACATGAAGGCAAATATTTGCTGTGTGAAGTATAATCCTGGATCAAGCAGCTATG

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|169083268|gb|FE491884.1|FE491884

EST:     ACAATGCTAGTGTCTGGGAGTGACGACGGAAAG                         GTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATG
genomic: ACAATGCTAGTGTCTGGGAGTGACGACGGAAAGgtagtgtttt ... tgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATG

EST: gi|169077264|gb|FE485150.1|FE485150

EST:     GGACGGACCCGACAATGCTAGTGTCTGGGAGTGACGACGGAAAG                         GTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATG
genomic: GGACGGACCCGACAATGCTAGTGTCTGGGAGTGACGACGGAAAGgtagtgtttt ... tgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATG

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: 35 (upstream exon), 35 (downstream exon)
Score: 20

AGTGTCATGGAGTACGAAGAGCACGAGAGAAGAGCCTGGAGCGTCGATTTCTCCAGGACGGACCCGACAATGCTAGTGTCTGGGAGTGACGACGGAAAGgtagtgtttt ... tgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

gtgttttattattacttacacacccgaattcactgtttgtgtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG