ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGCGCCACGATTAAAGGTCAATGCACTTTTTGGATGGCCTAGGGGGGACACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGgtcagcctcagaggtgtttgtgtttcttgagtgaactcctttttgaggacctatgcacctaattcatgatttccttaatcactcgtttatttcag

Basic information

species	Zea mays
transcript	GRMZM2G158097_T03
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G158097_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g36062.2 (Oryza sativa), 5'ss of exon 2

TGGCGCCACGATTAAAGGTCAATGCACTTTTTGGATGGCCTAGGGGGGACACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGgtcagcctcagaggtgtttgtgtttcttgagtgaactcctttttgaggacctatgcacctaattcatgatttc-cttaatcactcgtttatttcag----
 ||     |  |||||||| | |||| ||||||| |||  || ||| ||||| | | |||||||| ||| |||  |||||||||| ||||||||  |||||||||||||||||||||||      || | ||||||    |||  || || ||||||||| |||||||||||  | |||||| || ||  ||||||    
CGGGATTGCAGTTAAAGGTTACTGCAATTTTTGGGTGGATTAAGGGAGACACAAGAACACGTGAATTGAACCCATCTGCTGAATCATATACGCTTACAGGgtcagcctcagaggtgttt------ctcgggtgaacattgtttcaagtacatatgcacctgattcatgatttttcctaatcattcattggtttcaggcag

upper sequence: GRMZM2G158097_T03 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os04g36062.1 (Oryza sativa), 5'ss of exon 2

TGGCGCCACGATTAAAGGTCAATGCACTTTTTGGATGGCCTAGGGGGGACACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGgtcagcctcagaggtgtttgtgtttcttgagtgaactcctttttgaggacctatgcacctaattcatgatttc-cttaatcactcgtttatttcag
             |||||| | |||| ||||||| |||  || ||| ||||| | | |||||||| ||| |||  |||||||||| ||||||||  |||||||||||||||||||||||      || | ||||||    |||  || || ||||||||| |||||||||||  | |||||| || ||  ||||||
-------------AAAGGTTACTGCAATTTTTGGGTGGATTAAGGGAGACACAAGAACACGTGAATTGAACCCATCTGCTGAATCATATACGCTTACAGGGTCAGCCTCAGAGgtgttt------ctcgggtgaacattgtttcaagtacatatgcacctgattcatgatttttcctaatcattcattggtttcag

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|78092697|gb|DV521071.1|DV521071

EST:     ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGG                         GTAGGTGCAAAACCACGTGAGGTGTCTATATCTGTTGCTTCTTCAATCATG
genomic: ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGgtcagcctca ... tttatttcagGTAGGTGCAAAACCACGTGAGGTGTCTATATCTGTTGCTTCTTCAATCATG

EST: gi|89761707|gb|DY689615.1|DY689615

EST:     ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGG                         GTCAGCCTCAGAGGTAGGTGCAAAACCACGTGAGGTGTCTATATCTGTTGC
genomic: ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGgtcagcctca ... tttatttcagGT-AG-----G---T-G---CAAAACCACGTGAGGTGTCTATATCTGTTGC

EST: gi|71318422|gb|DR795977.1|DR795977

EST:     ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGGTCAGCCTCAGAG             
genomic: ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACG----C----T----CTCAG-Ggtcagcctca ..

EST: gi|76922721|gb|DV169140.1|DV169140

EST:     ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGGTCAGCCTCAGAG             
genomic: ACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACG----C----T----CTCAG-Ggtcagcctca ..

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), 35 (downstream exon)
Score: 27

TGGCGCCACGATTAAAGGTCAATGCACTTTTTGGATGGCCTAGGGGGGACACGACAGCACGTGAACTGATCCCTCCTGCTGAATCCTATACGCTCTCAGGgtcagcctca ... tttatttcagGTAGGTGCAAAACCACGTGAGGTGTCTATATCTGTTGCTTCTTCAATCATGGACATTCCTGCTGCGGATTGGGATGCCTGTGCGTGTGATTTAGATGATC

Block sizes: 49 (upstream exon), 34 (downstream exon)
Score: 22

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 24