ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagagattgatgcattttctttttgttccgttaattggctgttctgccatattgatctgttttaacctcttttagCCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCTTGCCATGCTTCCAAATGCCATTACATCCAG

Basic information

species	Zea mays
transcript	GRMZM2G039396_T01
intron #	4
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G039396_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 3'ss of exon 4

gtaagagattgatgcattttctt-tttgttccgttaattggctgttctgccatattgatctgttttaacctcttttagCCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCTTGCCATGCTTCCAAATGCCATTACATCCAG
    | || |||   |||  ||| ||||||   ||||||| |  || ||  | | |||| ||  || |||  ||||||||||||||| | |||||| ||||||||||||||||||||||||||||||||  | ||||| ||  |||| |||||||| ||
----gtgagtgagaaattgccttctttgttggattaattgtccattgtgttacactgatatgccttcaccatttttagCCGCCTTCCAACGCCAAAGGGGCAGACAGTTGCATCTTTCAGGAAGGGTCTGACTATGCTCCCGGATGCTATTACATCTAG

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|76286241|gb|DV025809.1|DV025809

EST:     ATCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCACCGAGGGATGC                         CCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCT
genomic: ATCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCACCGAGGGATGCgtaagagatt ... cctcttttagCCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCT

EST: gi|78079002|gb|DV507414.1|DV507414

EST:     ATCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCACCGAGGGATGC                         CCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCT
genomic: ATCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCACCGAGGGATGCgtaagagatt ... cctcttttagCCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCT

EST: gi|213183994|gb|FM183521.1|FM183521

EST:     ATCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCACCGAGGGATGC                         CCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCT
genomic: ATCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCACCGAGGGATGCgtaagagatt ... cctcttttagCCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCT

EST: gi|78087541|gb|DV515934.1|DV515934

EST:     TCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCATCCGAGGGATGC                         CCCGCCTTCCGAAGTCAAAAGG
genomic: TCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCA-CCGAGGGATGCgtaagagatt ... cctcttttagCC-GCCTTCCGAAGCCAAAAGG

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: 78

GGAAGGTTTGGCGGTTGGAAGAAACTGGAGGTAGTATTATTGGTGGAACCATCAAGACAATTCAGGAGAGGAGCAAGAATCCAAAACCACCGAGGGATGCgtaagagatt ... cctcttttagCCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCTTGCCATGCTTCCAAATGCCATTACATCCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 137

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 45

Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 83

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

ttttgttccgttaattggctgttctgccatattgatctgttttaacctcttttagCCGCCTTCCGAAGCCAAAAGGGCAGACAGTTGCATCTTTCAGGAAGGGTCTTGCCATGCTTCCAAATGCCATTACATCCAG