ERISdb: a Database of Plant Splice Sites

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

Sequence

atgc intronic sequence ATGC exonic sequence

gtaagtactggttcacttttcttcacatgatacacattctgcgattgttgacaagtgactaccttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGCCCTGTTGCTTACTTTTACTTCGATCCTTATTCAAGACCATCTGAAAAGC

Basic information

species	Zea mays
transcript	GRMZM2G133919_T01
intron #	9
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 9
lower sequence: LOC_Os02g58340.1 (Oryza sativa), 3'ss of exon 9

gtaagtactggttcacttttcttc---acatgatac----acattctgcgattgttgacaagtga-ctacctttt-cagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGCCCTGTTGCTTACTTTTACTTCGATCCTTATTCAAGACCATCTGAAAAGC
||||| | | |||  |||||||||   | |  |||     |  ||||||   | ||||| | |||  |||||||| ||| | ||| | ||||||||||||||||| ||||||||||| ||||| | ||||||||||||||| || ||||||||||| ||||||||||||||||| ||||
gtaagcagttgttttcttttcttcagcaaactatatgttaatgttctgcagctattgaccactgagttacctttttcagGTTTGGAATAGTGATGTCAAATTTTACTGTGTCAAAGATTCTTCGAATAGCCCTGTTGCTTATTTCTACTTCGATCCATATTCAAGACCATCTGAGAAGC

upper sequence: GRMZM2G133919_T01 (Zea mays), 3'ss of exon 9
lower sequence: Vv06s0061g01070.t01 (Vitis vinifera), 3'ss of exon 9

----------------------------gtaagtactggttcacttttcttcacatgatacacattctgcg-attgttgacaagtgactacc--ttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGCCCTGTTGCTTACTTTTACTTCGATCCTTATTCAAGACCATCTGAAAAGC
                             ||| | ||  || | |     | ||||  |  ||||| |||  |    ||| |  ||  |     | | ||| | ||| ||| ||||||||||||||||||||||||||| |||    | |  ||  | || ||||||||||| ||||| ||| |  | || || ||||| |
gtaatatactaatatctgttctcgttctttaatttctcatttattccgaataacat--tgaacattttgcataccaatgatatatggttcatgatctccagGTTTGGAACAATGATGTCAAATTTTATTGTGTCAAAGATTCTCTAGGCATTCCGATAGCATACTTTTACTTTGATCCATATGCTCGTCCTTCAGAAAAAC

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|28909606|gb|CB331010.1|CB331010

EST:     AAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCG                         ATCTGGCACAG-GATGTCAAATTTTATTG-GTCAAAGACTCTTCCAGTAGC
genomic: AAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC

EST: gi|67011759|gb|CO440508.1|CO440508

EST:     CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCG                         ATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC
genomic: CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC

EST: gi|31664241|gb|CD572966.1|CD572966

EST:     CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCG                         ATCTGGCACAG-GATGTCAAATTTTATTG-GTCAAAGACTCTTCCAGTAGC
genomic: CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC

EST: gi|67026706|gb|CO455455.1|CO455455

EST:     CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCG                         ATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC
genomic: CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC

EST: gi|211206209|gb|FL245888.1|FL245888

EST:     CACATAAGCTTTTTGAAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCG                         GTCTGGCACAGTGATGTCAAATTTTAYTGTGTCAAAGACTCTTCCAGTAGC
genomic: CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC

EST: gi|67025999|gb|CO454748.1|CO454748

EST:     ACATAAGCTTTTTGCCAG-TACTGTTGAACCTGCAGATGGGCTGGCTCCG                         ATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC
genomic: ACATAAGCTTTTTG-GAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC

EST: gi|15554185|gb|BI644183.1|BI644183

EST:     CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCG                         ATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC
genomic: CACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGC

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: 199

GCGCCCTTATTTTGCACTACCCAAGGTTATGGATGGCCTCTTCACTCTGGCACATAAGCTTTTTGGAGTTACTGTTGAACCTGCAGATGGGCTGGCTCCGgtaagtactg ... accttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGCCCTGTTGCTTACTTTTACTTCGATCCTTATTCAAGACCATCTGAAAAGC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 227

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 170

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 189

atgc intronic sequence ATGC exonic sequence

Intronic sequence truncated to 55 bases.

cttttcttcacatgatacacattctgcgattgttgacaagtgactaccttttcagATCTGGCACAGTGATGTCAAATTTTATTGTGTCAAAGACTCTTCCAGTAGCCCTGTTGCTTACTTTTACTTCGATCCTTATTCAAGACCATCTGAAAAGC