ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

TGGTTCTGTTGAAACCTCCATATCGTCCCATTTTGGAGGCATGAACTATCCATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattctactgcatctatgctatgttcatttctttggtgccgagaggagggtgtgctaaaaaaacatttacttaacattgttatctgagtttagacaaagcagatactgtaccatacaattttaaaccattttacagaatggatggatatggtttctgataggtttgcctttgcttcag

Basic information

species	Zea mays
transcript	GRMZM2G012319_T01
intron #	22
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 22
lower sequence: LOC_Os03g15900.2 (Oryza sativa), 5'ss of exon 20

TGGTTCTGTTGAAACCTCCATATCGTCCCATTTTGGAGGCATGAACTATCCATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtata-ttctactgcatctatgctatgttcatttctttggtgccgagaggagggtgtgctaaaaaaacatttacttaacattgttatctgagtttagacaaagcagatactgtaccatacaattttaaaccattttacagaatggatggatatggtttctgataggtttgcctttgcttcag
||||||||| ||||| |||||||||||||||||| | |||||||||||||| ||  |||||||||||||||| ||| |  ||||||| ||||||||||||||||  || ||||   ||| |    |||| |  |  |        |  ||        || || ||   ||     || |  ||  |   |   ||   ||                                                                                 
TGGTTCTGTAGAAACATCCATATCGTCCCATTTTAGTGGCATGAACTATCCGTCGTTGTTCAGTTCAAAACCATCAGGATATGGGGCTTCACAACAAACGgtattcttttacttagtctttttagtgttaaagtgatctccatt-attgggtttcacacttaataactgttggaa-aataacgtactgaaaacctatgaaat--------------------------------------------------------------------------------

upper sequence: GRMZM2G012319_T01 (Zea mays), 5'ss of exon 22
lower sequence: Vv07s0031g02090.t01 (Vitis vinifera), 5'ss of exon 23

TGGTTCTGTTGAAACCTCCATATCGTCCCATTTTGGAGGCATGAACTATCCATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatatt-ctactgcatctatgctatgttcatttct-ttggtgccgagaggagggtgt--gctaaaaaaacatttacttaacattgttatctgagtttagacaaagcagatactgtaccatacaattttaaaccattttacagaatggatggatatggtttctgataggtttgcctttgcttcag
 || || |||||||| || ||||| ||||| ||||| || ||||||||||||||  |||||||||||  ||||||  |  ||||| | ||||||    | |||| |  ||| | || | | | ||| || || ||| ||  |  | |   | |||| |    | |       | || |||| | | | |      || |                                                                                      
GGGATCAGTTGAAACTTCTATATCATCCCACTTTGGTGGAATGAACTATCCATCTTTGTTCAGTTCACGACCGTCTGGCTATGGGACTTCACAATCCTCAgtatgtaactaattcaacgaggttattttaatgtctgttattttctaagtgtgggtattgattgacctggtttctagttaagaatatgaaaaacattgaa-------------------------------------------------------------------------------------

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|211048296|gb|FL052136.1|FL052136

EST:     CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACG                         ATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA
genomic: CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA

EST: gi|74238553|gb|DT646467.1|DT646467

EST:     CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACG                         ATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA
genomic: CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA

EST: gi|22546271|gb|BU098582.1|BU098582

EST:     CATCATTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACG                         ATACGCGAAGAACCACCCTCATATTCGACGTCAGGAACTTACAGGAGGAAG
genomic: CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCA-GTAC-TACA-GAGGAAG

EST: gi|211051238|gb|FL052137.1|FL052137

EST:     CATCACTGTTCARTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACG                         ATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA
genomic: CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA

EST: gi|26558707|gb|CA830942.1|CA830942

EST:     CATCATTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACG                         ATACGCGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA
genomic: CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA

EST: gi|76909470|gb|DV163396.1|DV163396

EST:     CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACG                         ATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA
genomic: CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA

EST: gi|87156397|gb|DY401186.1|DY401186

EST:     CATCATTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACG                         ATACGCGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA
genomic: CATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAA

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: 430

TGGTTCTGTTGAAACCTCCATATCGTCCCATTTTGGAGGCATGAACTATCCATCACTGTTCAGTTCAAAACCGTCAAGTCATGGGGCCTCACAACAAACGgtatattcta ... tttgcttcagATACGTGAAGAACCACCCTCATATTCGACGTCAGTACTACAGAGGAAGGAATCATTTGAAAACCCCCTTGGAGGGGGTGGAGGACGAAGTTTCGGATCCC

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 358

Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 501