ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttccttccgtcatccgcactaccttgtcccttcggcggccttcgacttgtctagatctcggggggagttggcgcgcttctccgatccgatcac...

Basic information

species	Zea mays
transcript	GRMZM2G174730_T02
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G174730_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g42330.2 (Oryza sativa), 5'ss of exon 1

-CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGG-AGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtg-----ttccttccgtcatccgcactaccttgtcccttcggcggccttcg--acttgtctagatctcggggggagttggcgcgcttctccgatccgatcac
 |  |    |   || |||||  |||  |||| ||| ||||||| ||||||||||||||||| |||||||||||||| |||||| ||||||| || |||||||||||||     | ||   |||    | | |   || ||   ||||      ||||    | |  |||||||||||| | |||  |   ||  || ||||       
TCGTCGTTGCCGTCGTCGCCGTCGGC--GGAGTAGGCAGGCGGCCATGGCGGGGAAGCACGGCCGCAACGGCTTCGAGGACGACGACGTCAATCCCTTCGCGgtgagtgctcgctccccctcgttccacccccgcgctagtatattcgagaaggttcgctgttcgcgtagatctcggggtgggttctc---ctgatctgatctac----

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|211137750|gb|FL292365.1|FL292365

EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

EST: gi|91876331|gb|EB406288.1|EB406288

EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

EST: gi|149015443|gb|EE045301.2|EE045301

EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

EST: gi|211341624|gb|FL411903.1|FL411903

EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCA
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCA

EST: gi|211137751|gb|FL292366.1|FL292366

EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACNACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

EST: gi|211138689|gb|FL292372.1|FL292372

EST:     GGAAGCACGTGCGCAACGGCTTCGACGACGACNACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

EST: gi|211138692|gb|FL292375.1|FL292375

EST:     GAAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: G-AAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

EST: gi|211138694|gb|FL292377.1|FL292377

EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

EST: gi|211138693|gb|FL292376.1|FL292376

EST:     GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCG                         GGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT
genomic: GGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACAT

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: 47 (upstream exon), 49 (downstream exon)
Score: 357

CAGCCCACCACCCGACGCCGGAGGCCCGGAGGAGGAGGCGGCGATGGCGGGGAAGCACGGGCGCAACGGCTTCGACGACGACAACGTCAACCCTTTCGCGgtgagtgttc ... tatcttgcagGGAGGAAGTGTTCCACCTGCCACCAATTCTCGTCTCTCACCTCTATCACATGAACCGGCTGATTTCTACAATGTGGACATTCCTCTCGACTCATCAAAG

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 256

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 175