ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq
PPT, BS, UA-tract

Sequence

atgc intronic sequence ATGC exonic sequence

gtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT

Basic information

species	Zea mays
transcript	GRMZM2G410515_T02
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G410515_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g08570.1 (Oryza sativa), 3'ss of exon 4

---------------------------------------gtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgatttttt----------atgcattga-tagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT
                                          |  | | |  ||   |   || || |   | ||| ||| ||||  ||||||||||   |||||||||   ||  || ||||||          |||| ||||  || |||||||||||||||||||||||||||||||||| || |||||||||||||||||||                                          
gttttactcttatgcttttatgttgcatttaattttttttgttattcattctttttttttttggttgcctttatcttaatagctcatattcactgttagtagcatttgtggattattgtttttttttttggggaaatgccttgaacagATAGCTGCTTGGAAGGATGAAGATGGAGATTGGTATGAAACTGGGCTTCATATCTTTT------------------------------------------

upper sequence: GRMZM2G410515_T02 (Zea mays), 3'ss of exon 4
lower sequence: AT4G14210.2 (Arabidopsis thaliana), 3'ss of exon 4

--gtctgataaatac-ttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT
   |||| |   ||  ||   |   |||||  | |  | | |     |  |  ||    |    |||  |  ||||  | |||| |||  |        || ||||||| ||||||||||||||||| || ||||| ||||||||  | ||||| || |                                          
ttctctggttcttaggttaggttcttgtttgttccgttttaacaatttacctatcttattggagagcgatatttatgatgtgatattt-gtcttcctccagATAGCTGCATGGAAGGATGAAGATGGGGACTGGTATGAGACTGGTTTACATATTTTCT------------------------------------------

upper sequence: GRMZM2G410515_T02 (Zea mays), 3'ss of exon 4
lower sequence: EDP05305 (Chlamydomonas reinhardtii), 3'ss of exon 1

gtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT--
      | | |     |  | | |    | | |   || || | |  |||  |  |      |   |     |   |  |  ||||      || ||||| ||||| ||||||||||| ||||| || ||||||||||||||  | || ||||| |         |   |    | |   |    ||||||      |  
-----gtgagtgtgcacccggc-gagcgccaattcgtgcatcg-tagcataaatggacaattgggctaaccgtgcca--accttttgc----tggtagGTCGCTGCATGGAAGGATGAGGATGGCGACTGGTACGAGACTGGCTTGCACATCTTCTTCGGCGCGTA--CCCCAACATGATGAATGTCTTCAAGGAGCTAA

upper sequence: GRMZM2G410515_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ23885 (Selaginella moellendorffii), 3'ss of exon 4

gtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT
                                     | || | | | |  | || ||||  ||   ||| | || | || |     |      |||||| || |||||||||||  ||||||| |||||||| ||||| || |||||||| || |                                          
--------------------------------gtcgggtatagttttaaaactct-tttttggc---tgtaacttaacgactgaagctaacgatatagGTGGCAGCTTGGAAGGACAAAGATGGCGATTGGTATGAGACCGGCCTTCATATTTTCT------------------------------------------

upper sequence: GRMZM2G410515_T02 (Zea mays), 3'ss of exon 4
lower sequence: EFJ10018 (Selaginella moellendorffii), 3'ss of exon 3

gtctgataaatacttgcatgactgtttactactctctgaattgctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT
                                     |  | | | | |  | || ||||  ||   ||| | || | || |     |      |||||| || |||||||||||  ||||||| |||||||| ||||| || |||||||| || |                                          
--------------------------------gtcgggtgtagttttgaaactct-tttttggc---tgtaacttaacgactgaagctagcgatatagGTGGCAGCTTGGAAGGACAAAGATGGCGATTGGTATGAGACCGGCCTTCATATTTTCT------------------------------------------

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|211417844|gb|FL018174.1|FL018174

EST:     TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGGTGGAAAA                         GTAGCTGCTTGGAAGG
genomic: TGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGG-TGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGG

EST: gi|211417848|gb|FL018178.1|FL018178

EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGNAT-GGTACGAGACTGGGCTTCA
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAG-ATTGGTACGAGACTGGGCTTCA

EST: gi|211417840|gb|FL018170.1|FL018170

EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT

EST: gi|211417841|gb|FL018171.1|FL018171

EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAG
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAG

EST: gi|74236167|gb|DT644081.1|DT644081

EST:     CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAG                         GTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT
genomic: CTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCAT

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: 46 (upstream exon), 45 (downstream exon)
Score: 56

GATTGGCTGGTCTATCAACAGCGAAGTATCTGGCAGATGCTGGACATAAACCCATATTGCTTGAGGCAAGAGATGTTTTGGGTGGAAAGgtctgataaa ... gcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 167

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 105

Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 160

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ctctcattcactgttttcagcatttgttattttatgattttttatgcattgatagGTAGCTGCTTGGAAGGATGAAGATGGAGATTGGTACGAGACTGGGCTTCATATCTTTTGTAAGTTACAGTTCTGGTCCTTGAGGTCCTCTTCATCATATT