ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TATCAAAATCTATCAACTTCGTGCACACACGGAGAAATCTTGTTGAAAATGACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcgttttatttattttttaggtcaattgcagtagttatactgaatctggccagaaactgcttcaacacgaaagagatattgtctacatttttttactctgtttatttcagttggaatatttgttctatctggtcaaatgaatgtgttttcagaacacgtactgatatggcatgtctttgtgtag

Basic information

species	Zea mays
transcript	GRMZM2G055917_T02
intron #	8
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G055917_T01 (Zea mays), 5'ss of exon 8
lower sequence: LOC_Os09g21780.1 (Oryza sativa), 5'ss of exon 8

TATCAAAATCTATCAACTTCGTGCACACACGGAGAAATCTTGTTGAAAATGACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg-ttttatttattttttaggtcaatt-gcagtagtta--tactgaatctggccagaaactgcttcaacacgaaagagatattgtctacatttttttactctgtttatttcagttggaatatttgttctatctggtcaaatgaatgtgttttcagaacacgtactgatatggcatgtctttgtgtag
|||||||  |||| || || |||||||| ||||||||||| ||||| ||||| ||||||||||||||||| ||||||||||||||||| |||||||||||||||  ||   ||||| ||| | |||   |   ||  || ||| ||  |||||||||  || ||||    ||  ||||  || ||||| |  | |  ||   |                                                                                            
TATCAAAGGCTATTAATTTGGTGCACACGCGGAGAAATCTGGTTGAGAATGATCGTGTTTTGCTGAACCGAGCACATCGTGCTCAACAGGAATATGAAAGgtacgctgaaattttacttaatctttgtctttcttcacaatagatatttactgaatccagctagaa----ctgtaacataaaggagatgtcttgtgtatcagtg-------------------------------------------------------------------------------------------

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|211501174|gb|FL470499.1|FL470499

EST:     ACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGA
genomic: ACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATG-AAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGA

EST: gi|60350836|gb|DN217809.1|DN217809

EST:     CGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG
genomic: CGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG

EST: gi|60397456|gb|DN230272.1|DN230272

EST:     GAACCGTGCACATCGTGTTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG
genomic: GAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG

EST: gi|60396367|gb|DN229236.1|DN229236

EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG

EST: gi|74234255|gb|DT642169.1|DT642169

EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG

EST: gi|211501173|gb|FL470498.1|FL470498

EST:     GA-CGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGGCTGGTGA
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAA-GCTGGTGA

EST: gi|24765164|gb|CA400324.1|CA400324

EST:     GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAG                         AGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG
genomic: GACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAG

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: 49 (upstream exon), 49 (downstream exon)
Score: 93

TATCAAAATCTATCAACTTCGTGCACACACGGAGAAATCTTGTTGAAAATGACCGTGTTTTGCTGAACCGTGCACATCGTGCTCAACAAGAATATGAAAGgtacattgcg ... ctttgtgtagAGTGGCCAACTATTGTCTTAAATTAGCTGGCGAACAAGAAAAGCTGGTGAGTGAAAGATGGCTTCCGGAGCTGAGAAATGCAGTTCAAGAAGCTCGGAGG

Block sizes: 47 (upstream exon), 46 (downstream exon)
Score: 20

Block sizes: 46 (upstream exon), 46 (downstream exon)
Score: 20