ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

ATGGAGCTTTGCTAGTTACTGGCTCTGCGGACAAAAATTTGAAGATATGGGGTATGGATTTTGGGGACTGCCACAGGTCTATATTTGCTCACTCAGACAGgtatgatattgcctttttaatcattgtttttcgttttgattataggcagaaccttatattttttggatgtcttcactttgcag

Basic information

species	Zea mays
transcript	AC209858.4_FGT002
intron #	5
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC209858.4_FGT002 (Zea mays), 5'ss of exon 5
lower sequence: LOC_Os03g05720.1 (Oryza sativa), 5'ss of exon 5

ATGGAGCTTTGCTAGTTACTGGCTCTGCGGACAAAAATTTGAAGATATGGGGTATGGATTTTGGGGACTGCCACAGGTCTATATTTGCTCACTCAGACAGgtatgatattgcctttttaatcattgtttttcgttttgattataggcagaa-ccttata--ttttttggatgtcttcactttgcag
|||||| | |  |||||||||| ||||| |||||||||||||| || ||||||||||||||||| |||||||| | |||||||||||| ||| | |||||||    | ||||| ||||  |   |  |||  | ||||| | | |||| || ||||| |  |||||   | || |||| |||||||
ATGGAGTTCTAATAGTTACTGGTTCTGCAGACAAAAATTTGAAAATTTGGGGTATGGATTTTGGTGACTGCCATAAGTCTATATTTGCCCACACGGACAGgttatttcttgcccttttgtt---ttctttgtgatttgactgttggcacaatccttacacctttttctcacgtgttcaatttgcag

upper sequence: AC209858.4_FGT002 (Zea mays), 5'ss of exon 5
lower sequence: AT3G21540.1 (Arabidopsis thaliana), 5'ss of exon 5

ATGGAGCTTTGCTAGTTACTGGCTCTGCGGACAAAAATTTGAAGATATGGGGTATGGATTTTGGGGACTGCCACAGGTCTATATTTGCTCACTCAGACAGgta----------tgatattgcctttttaatcattgtttttcgttttgattataggcagaaccttatattttttggatgtcttcactttgcag--------
||||||  ||| | |||||||| |||  ||||||||||||||| || |||||| |||||||||| || || || | |||||| ||||||||    ||||||||          |  ||     ||| | |  || |  |  |||  | | || | |  || ||   | ||  ||| || |  | | ||||           
ATGGAGAGTTGATTGTTACTGGTTCTCAGGACAAAAATTTGAAAATTTGGGGTTTGGATTTTGGTGATTGTCATAAGTCTATCTTTGCTCATGGTGACAGgtacttccataattcgtaccatatttctgaaaatggcataacgtactcaata-atgtggacccagtttttccttgaatattataattttgtgtaagaaaac

upper sequence: AC209858.4_FGT002 (Zea mays), 5'ss of exon 5
lower sequence: Vv08s0007g04690.t01 (Vitis vinifera), 5'ss of exon 5

ATGGAGCTTTGCTAGTTACTGGCTCTGCGGACAAAAATTTGAAGATATGGGGTATGGATTTTGGGGACTGCCACAGGTCTATATTTGCTCACTCAGACAGgtatgatattgcctttttaatcattgtttttcgttttgattataggcagaaccttatattttttggat--gtcttcactttgcag--------------------------------
|||||| |||||| || ||||| ||||| ||||||||||||||||| |||||| |||||||||| || ||||| |  ||||| ||||||||  | || ||||       | | | |||||  ||    |||    ||   ||| |     |  ||| ||  | |      ||  | |||| ||||                                
ATGGAGATTTGCTTGTCACTGGTTCTGCAGACAAAAATTTGAAGATTTGGGGTTTGGATTTTGGTGATTGCCATAAATCTATTTTTGCTCATGCTGATAGgtg-----cttcatatttaaaaataaaatttaagatttgatattgtttagagtttagatgatgtaagccagttgttacttagcagttgtgaatttctcataagcatttttatggcag

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|148933242|gb|EC876892.2|EC876892

EST:     GGTATGGATTTTGGGGACTGCCACAGGTCTATATTTGCTCACTCAGACAG                         TGTGATGGATGTTAAGTTTGTGTATAGAACTCATTATATGTTCAGTGTGGG
genomic: GGTATGGATTTTGGGGACTGCCACAGGTCTATATTTGCTCACTCAGACAGgtatgatatt ... cactttgcagTGTGATGGATGTTAAGTTTGTGTATAGAACTCATTATATGTTCAGTGTGGG

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: 191

ATGGAGCTTTGCTAGTTACTGGCTCTGCGGACAAAAATTTGAAGATATGGGGTATGGATTTTGGGGACTGCCACAGGTCTATATTTGCTCACTCAGACAGgtatgatatt ... cactttgcagTGTGATGGATGTTAAGTTTGTGTATAGAACTCATTATATGTTCAGTGTGGGGAAAGATCGCACTATGAAGTACTGGGATGCTGATAAATTTGAGTTATTG

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 104

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 119