ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctgctcgccccaaccatttccctgaacatccagtctccaagactccaacaaaacggggcagagtcaccctgctgaagaattggattttccgattactattttgctaacatgacgagttaattgtctcag

Basic information

species	Zea mays
transcript	AC233960.1_FGT002
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: AC233960.1_FGT002 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os02g47200.1 (Oryza sativa), 5'ss of exon 2

GATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctgctcgccccaaccatttccctgaacatccagtc--tccaagactccaa-caaaacggggcagagtcaccctgctgaagaattggattttccgattactattttgctaacatgacgagttaattgtctcag
|||||| || || |  |||||||| || |||||||||||||||||| ||||||| |||||||||||    |||||||||||||| ||||| ||||||||||| | |      | |  | |   || |    || |||  | |  || |     |  | | ||| ||    || |||          |||   |||||| |                                       
GATCGACCTGAAGAAGCACCACGAGCCGAAGGTGCTGCTCGACAAGGTCGCCTACTGGACCGTCAAGGCGCTGCGCGTGCCCACTGACATCTTCTTCCAGgtaacc---aaccacaactaattttccatcaaagatcatgccaatctattttgctgatcgaaatggatgggaatcaat-------ggaac--gattttgcag-------------------------------------

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|78107637|gb|DV526055.1|DV526055

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|149099036|gb|EE185054.2|EE185054

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|71422715|gb|DR805803.1|DR805803

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|71764916|gb|DR962853.1|DR962853

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|149095769|gb|EE181412.2|EE181412

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|148937945|gb|EC882176.2|EC882176

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATG

EST: gi|149096470|gb|EE182212.2|EE182212

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|89249421|gb|DY621207.1|DY621207

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|76015230|gb|DT942400.1|DT942400

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|76017432|gb|DT944602.1|DT944602

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|78107664|gb|DV526082.1|DV526082

EST:     CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAG                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG
genomic: CCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCG

EST: gi|149078562|gb|EE167345.2|EE167345

EST:     CTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTTCTTCCAA                         AGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGC
genomic: CTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATT-CTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGC

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: 39 (upstream exon), 38 (downstream exon)
Score: 8

GATCGATCTCAACAGACACCACGAACCCAAGGTGCTGCTCGACAAGATCGCCTATTGGACCGTCAAATTACTGCGCGTGCCCACCGACATATTCTTCCAGgtgatccctg ... attgtctcagAGGAGGTACGGCTGCCGTGCTATGATGCTGGAAACAGTGGCGGCGGTGCCGGGGATGGTGGGCGGCATGCTGCTTCACCTGCGCTCGCTCCGCCGCTTCG

Block sizes: 47 (upstream exon), 45 (downstream exon)
Score: 41

Block sizes: 45 (upstream exon), 48 (downstream exon)
Score: 71