ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GCCTCGCGTTCCGTCTCCGAAGCCGCAGGCAGCCATGGAAATCAACGAGGAGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGACgtaagtccctcccctcgccgtcccgagcgccgccgcggttcgcagggtcctcggctgacgttcttgccttccgccgcag

Basic information

species	Zea mays
transcript	GRMZM2G100639_T01
intron #	1
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G100639_T01 (Zea mays), 5'ss of exon 1
lower sequence: LOC_Os05g39850.1 (Oryza sativa), 5'ss of exon 1

----GCCTCGCGTTCCGTCTCCGAAGCCGCAGGCAGCCATGGAAATCAACGAGGAGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGACgtaagtccctcccctcgccgtcccgagcgccgccgcggtt--cgcagggtcctcggctgacgttcttgccttccgccgcag------
    | | ||||| ||||||||| |||     |||||||||||  ||||||||||||||||||||||||| |||||||| |||||||||||||||||||| || || |||||||| |  || ||    |    ||||||| |    ||| | || ||| |    |||   || |  |||  |||       
TCCGGTCGCGCGTCCCGTCTCCGGAGC----AGCAGCCATGGACGTCAACGAGGAGGCAATGGCGGCGCACAAGCGCGCGTTCCTCGACTTCCTCGACCAGGATgtgagtccctctcgccgtcgctttgcctcccgccgccgccgccgccgtgttctccggatccgtggctgacgcccgttgcatctgcag

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|211158414|gb|FL068719.1|FL068719

EST:     AGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGAC                         GTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAAG
genomic: AGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGACgtaagtccct ... tccgccgcagGTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAAG

EST: gi|30306471|gb|CD001144.1|CD001144

EST:     AGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGAC                         GTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAAG
genomic: AGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGACgtaagtccct ... tccgccgcagGTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAAG

EST: gi|18450616|gb|BM428894.1|BM428894

EST:     GCATATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGTAC                         GTCGGTAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAA
genomic: GCA-ATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAG-ACgtaagtccct ... tccgccgcagGTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAA

EST: gi|74233767|gb|DT641681.1|DT641681

EST:     AGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGAC                         GTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAAG
genomic: AGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGACgtaagtccct ... tccgccgcagGTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAAG

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), 48 (downstream exon)
Score: 435

GCCTCGCGTTCCGTCTCCGAAGCCGCAGGCAGCCATGGAAATCAACGAGGAGGCAATGGCGGCGCATAAGCGCGCCTTCCTCGACTTCCTCGACCAAGACgtaagtccct ... tccgccgcagGTCGGGAAGGGGGTTTACATGCAGGCCGTCCGCGACATGGTCCAGAACAAGCGCCACCGCCTCATCATCGGCATGGACGACCTCCGCAATCACAATCTCG

Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 46

Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 15