ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtaagcgctcgatctctcttcccatttcctcagcgattggtagcgatttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA

Basic information

species	Selaginella moellendorffii
transcript	EFJ07968
intron #	1
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: EFJ07968 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G106574_T01 (Zea mays), 3'ss of exon 2

----------------------------------------gtaagtaag--cgctcgatctctcttcccatttcctcagcgattggtagcgatttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA
                                         ||  || |   |||     | |     || |   ||    |    |  | ||||  |  |||| |||||| |||||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || ||  |   | ||||              
actttggctcaactggatcttagtcttcactgttcattcaatagctaggtttgctgacattttgaggacaatatttctaacacaatttaccattt--taaagGCTAGCGATAGATTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT--------------

upper sequence: EFJ07968 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G121942_T03 (Zea mays), 3'ss of exon 2

-------------------------gtaagtaagcgctcgatctct----cttcccatttcctcagcg----attggtagcg--atttcttgc-----agGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA
                          | |||   || ||  |  ||     |||  |  |  |||  |    | || || |   ||||  |       |||| |||||| | |||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || ||  |   | ||||              
ttaaaggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaagGCTAGCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT--------------

upper sequence: EFJ07968 (Selaginella moellendorffii), 3'ss of exon 1
lower sequence: GRMZM2G121942_T01 (Zea mays), 3'ss of exon 2

--------------------gtaagtaagcgctcgatctc----tcttcccatttcctcagcg----attggtagc--gatttcttgc-----agGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA
                     | |||   || ||  |  |    | |||  |  |  |||  |    | || || |   ||||  |       |||| |||||| | |||||||||||||| ||||| |||||||| || ||||| ||||| || || ||||| || ||  |   | ||||              
ggttcaactggatcttagtcttcagtgttcgttcagtagctaggttttctgacattttcaatgcaatactgctaacacaatttactatttgaaaggctagCGATAGGTTCAACATAAACTCTCAGCTTGAGCATCTTCAAGCCAAATATGTTGGTACAGGGCATGCTGATTTGTCTAGATT--------------

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|70669179|gb|DN837756.1|DN837756

EST:     AGGGCCTAGGGTTTGTGGTTTTCTTGGGGAGCAAGCACGATGCAG                         GCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG
genomic: AGGG-CTAGGGTTTGTGGTTTTCTTGGGGAGCAAGCACGATGCAGgtaagtaagc ... tttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG

EST: gi|70669222|gb|DN837799.1|DN837799

EST:     AGGGCTAGGGTTTGTGGTTTTCTTGGGGAGCAAGCACGATGCAG                         GCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG
genomic: AGGGCTAGGGTTTGTGGTTTTCTTGGGGAGCAAGCACGATGCAGgtaagtaagc ... tttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG

EST: gi|169095878|gb|FE498920.1|FE498920

EST:     GGTTTGTGGTTTTCTTGGGGAGCAAGCACGATGCAG                         GCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG
genomic: GGTTTGTGGTTTTCTTGGGGAGCAAGCACGATGCAGgtaagtaagc ... tttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG

EST: gi|169081458|gb|FE487719.1|FE487719

EST:     CAAGCACGATGCAG                         GCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG
genomic: CAAGCACGATGCAGgtaagtaagc ... tttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG

EST: gi|169032450|gb|FE436684.1|FE436684

EST:     GTTTTCTTGGGGAGCAAGCACGATGCAG                         GCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG
genomic: GTTTTCTTGGGGAGCAAGCACGATGCAGgtaagtaagc ... tttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAG

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: 42

TAGGGCTAGGGTTTGTGGTTTTCTTGGGGAGCAAGCACGATGCAGgtaagtaagc ... tttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA

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atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

taagcgctcgatctctcttcccatttcctcagcgattggtagcgatttcttgcagGCCAGCGATCGATTCAACATAAACTCGCAGCTAGAGCATCTCCAGGCCAAGTATGTGGGCACTGGGCACGCCGACCTCAATCGATTCGAGTGGGCGGTGA