ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GTCTCACGGCACGAATAATTGACGAGACAAATTCAATGTCAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatatatggagcactattgttgctgcagcctacatggagtctgagttgcctgtatataactgaacattcatactatttatagcattcctttgtaat...

Basic information

species	Zea mays
transcript	GRMZM2G029396_T02
intron #	6
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G029396_T02 (Zea mays), 5'ss of exon 6
lower sequence: LOC_Os03g59040.1 (Oryza sativa), 5'ss of exon 10

GTCTCACGGCACGAATAATTGACGAGACAAATTCAATGTCAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatatatggagc--actattgttgctgcagcctacatggagtctgagttgcctgtata--taactgaacattcatactatttatagcattcctttgtaat--
| ||||| |||||| ||||||| ||||||||  |||||||||| |||||||| |||||||||||||| |||||  ||||||| || ||||||      |||       |||   |   || ||  |   ||  |      |   |  ||||  |||    ||| ||| | |||||    ||||  |||  |||  
GGCTCACTGCACGAGTAATTGATGAGACAAACACAATGTCAGATGTCTATACTGCTTTCTATGAGTTCTCTTCGCTGATAGAATCGAAGgtaaggaccatgatctttgctaccatgaatgtagggtggctgtcgctcatttcttccatatagataataagacactcaaa-tattt----cattt-tttacaatag

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|211024645|gb|FL381982.1|FL381982

EST:     AGACGTCTATACCNGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA
genomic: AGACGTCTATACC-GCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA

EST: gi|61118554|gb|DN559515.1|DN559515

EST:     CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTG
genomic: CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTG

EST: gi|5791416|gb|AI978208.1|AI978208

EST:     ATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA
genomic: ATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA

EST: gi|5929059|gb|AW056351.1|AW056351

EST:     CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA
genomic: CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA

EST: gi|60338190|gb|DN205163.1|DN205163

EST:     CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA
genomic: CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA

EST: gi|211142093|gb|FL424854.1|FL424854

EST:     CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACNATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA
genomic: CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA

EST: gi|61118553|gb|DN559514.1|DN559514

EST:     CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTG
genomic: CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTG

EST: gi|60399247|gb|DN232061.1|DN232061

EST:     CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA
genomic: CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA

EST: gi|6022598|gb|AW067410.1|AW067410

EST:     CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAG                         ATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA
genomic: CAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCA

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: 48 (upstream exon), 49 (downstream exon)
Score: 116

GTCTCACGGCACGAATAATTGACGAGACAAATTCAATGTCAGACGTCTATACCGCTTTCTATGAGTTTTCTTCATTGATAGAGTCAAAGgtacaatata ... tatgttccagATTGATGACAATGATCCAAATGCTGCTCTAACACGGAGACACGTGAATTCAATAAAGCAAACTTGCAAGTCATCTGGTTTGGTAAAGAGGAG

Block sizes: 49 (upstream exon), 45 (downstream exon)
Score: 104

Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 99