ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtgagcttccatctctttttttcttttttccctggttttgtcttagtaaacgctctcggccaagtgaacttttcatgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG

Basic information

species	Selaginella moellendorffii
transcript	EFJ33488
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 4

gtgagcttccatct-ctttttttcttttttccctggttttgtct-tagtaaacgctctcggccaagt--gaacttttcatgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG
|||| | ||| ||  || | | |  |  | |  |  |    | |    ||| | ||      || ||   ||| ||| ||   |||||||| ||  |||| ||    ||||||||||| |  |||||||| |||||||| ||||||||||||
gtgatcatccttcaactgtatatgctgatgctgttataaattgtgcgataatcactgcaacacatgtccaaacgtttaattg-cagGAGCCAGTGATTCCCGGCTGCTTTCTCCGAGCTAGGGCCATCGGACTCATGCCCATGATCGATCAG

upper sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA19G35710.1 (Glycine max), 3'ss of exon 7

--------------gtgagcttc-catctctttttttcttttttccctggttttgtcttagtaaacgctctcggccaag--tgaactttt-catgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG
              ||   |||   ||    | | |  |  |||   |  | |    || |||||   |      |||   | ||||  | | |||||||||||| |||||||||||    ||||| || |||||||| || || |||||||| ||||| ||||||
tggatcttgtcgttgtcgtcttagtattaaatctgtcttaatttatgttatgtatgttttgtaaattgtaagattcaaaacttaactcatacttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG

upper sequence: EFJ33488 (Selaginella moellendorffii), 3'ss of exon 4
lower sequence: GLYMA03G33000.4 (Glycine max), 3'ss of exon 7

gtgagcttccatctctttttttctttttt--ccctggttttgtcttagtaaacgct-------ctcggccaagt---gaacttt--tca----tgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG
   |   |  ||||  || ||    | ||     |   ||| ||||| |  | | |       ||  |  |  |    ||||||  |||    |||||||||||| |||||||||||    ||||| || |||||||| || || |||||||| ||||| ||||||
acaattatggatcttattattatcatcttagtattaaatttttcttaatttatgttatgtatgcttcgtaagattcaaaactttactcatacttgaacagGAGCCGGTTCTTCCAGGTTGCTTTCTTCGGGCCAAAGCAATTGGTCTCATGCCCATGATTGATCAG

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|169098914|gb|FE502311.1|FE502311

EST:     GCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGATCATGCAA                         GAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATG
genomic: GCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGATCATGCAAgtgagcttcc ... tcatgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATG

EST: gi|169050028|gb|FE460096.1|FE460096

EST:     GCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGATCATGCAA                         GAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATG
genomic: GCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGATCATGCAAgtgagcttcc ... tcatgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATG

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), 25 (downstream exon)
Score: 3

AGTCCTTTATTCCTCGGTGGTTTATCCACACAACTATGGATTTGTTCCACGCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGATCATGCAAgtgagcttcc ... tcatgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttccctggttttgtcttagtaaacgctctcggccaagtgaacttttcatgaacagGAGCCTGTTCTTCCAGGAGCGTTTCTCCGAGCCAAAGCCATCGGGCTCATGCCGATGATCGATCAG