ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttggtagaattatccaagaggacctaactgagttcagcactgattttctttccttgtaaaaaataattccacttgtttggagttcacacattga...

Basic information

species	Zea mays
transcript	GRMZM2G132712_T03
intron #	27
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G132712_T03 (Zea mays), 5'ss of exon 27
lower sequence: LOC_Os08g40530.1 (Oryza sativa), 5'ss of exon 11

GCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgttt------ggtagaattatccaagaggacctaactgagttcagcactgattttctttccttgtaaaaaataattccacttgtttggagttcacacattga
|||||||||||||| |||||||||||||| |||||||||||||| |||||||| |||||||||||||||||||||||  ||||||| |||||||| |||||||||||      |    || ||| |  ||  ||||     | |  || |     |  ||   |    |  |   |||||| | |      |    | |      
GCCGATATAGGTCTCTCAATGGGCATTTCAGGGACAGAAGTTGCCAAAGAAAGTTCTGACATTATAATCTTGGATGACAACTTCACATCAGTTGTGAAGgtttgtttttccccgaacaaactattctggaatacct--tctaatgaaggataatgtcactaagcaaacaccatggaattcctcataccctcacactaaatt----

upper sequence: GRMZM2G132712_T03 (Zea mays), 5'ss of exon 27
lower sequence: EFJ22392 (Selaginella moellendorffii), 5'ss of exon 22

GCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttggtagaattatccaagaggacctaactgagttcagcactgattttctttccttgtaaaaaataattccacttgtttggagttcacacattga
|| ||||| |||||||||||||||||    ||||| || || || ||||||||||| |||||||||||  |||||||  ||||  | || |||||||||||  | |    | |  | |    | |   || |        || |  ||  ||||| |                                          
GCTGATATCGGTCTTTCAATGGGCATCCAAGGGACCGAGGTGGCCAAAGAAAGCTCAGACATTATAATTCTGGATGACAACTTTGCATCTGTTGTCAAGgtaagata---acagcttttggtgcgagtctga--------aggatcgaaattcttgcag----------------------------------------

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|211501925|gb|FL162234.1|FL162234

EST:     AAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAG                         GTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAG
genomic: AAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttgg ... tctctttcagGTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAG

EST: gi|5846827|gb|AI999910.1|AI999910

EST:     AAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAG                         GTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAG
genomic: AAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttgg ... tctctttcagGTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAG

EST: gi|5325014|gb|AI783205.1|AI783205

EST:     AAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAG                         GTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAG
genomic: AAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttgg ... tctctttcagGTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAG

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: 46 (upstream exon), 47 (downstream exon)
Score: 108

GCCGATATAGGTCTTTCAATGGGCATTTCCGGGACAGAAGTTGCTAAAGAAAGCTCTGACATTATAATCTTGGATGATGACTTCACGTCAGTTGTCAAGgtttgtttgg ... tctctttcagGTTGTTCGTTGGGGACGATCTGTCTACGCTAATATCCAGAAATTCATTCAGTTCCAGCTCACCGTCAATGTTGCTGCACTTGTCATTAATGTGGTTGCTG

Block sizes: 44 (upstream exon), 49 (downstream exon)
Score: 123

Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 172