ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

gcaagtgaagtcaactctcccctcctccccttccgcttccgcttccgcaaccgcattcgcgactctcggcctcccgtcccgcgccctcaacttgtcctctgccgctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGGAGAACGAGTTCAACTGGAGCGACAAGCACGACTCCCAGTACCTCGCCGA

Basic information

species	Zea mays
transcript	GRMZM2G113137_T01
intron #	2
splice site	3'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G113137_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g62090.1 (Oryza sativa), 3'ss of exon 2

gcaagtgaagtcaactctcccctcctccccttccgcttccgcttccgcaaccgcattcgcgactctcggcctcccgtcccgcgccctcaacttgtcctctgccgctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGGAGAACGAGTTCAACTGGAGCGACAAGCACGACTCCCAGTACCTCGCCGA
                             | ||  |  ||||     |  ||| |||  |  | ||| | |    | | | ||||  |  |  ||  |   | | | | | |||| ||||| ||||| ||||| || ||||||||||| | ||||||||||||||||||||||||||||||||| ||||||  |||||| |||||  |||||||
-------------------------gtaacctcgccgcccgcaatgcccgccggatttaccgccctccgtcggttg-ctcacgcctccccccggtggtt--ctggtttct-cagGTTGCGCCCGCGTCCCCGGCGATGAGGAGGAGGAGGACGTCGACGACCTGGAGAACGAGTTCAACTGGAGGGACAAGACCGACTCGCAGTATGTCGCCGA

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|32839810|gb|CD979491.1|CD979491

EST:     GCAAGACCCGCTTCAAGCGCCTCAAGG                         GGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG
genomic: GCAAGACCCGCTTCAAGCGCCTCAAGGgcaagtgaag ... ctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG

EST: gi|211327285|gb|FL017205.1|FL017205

EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGG                         GGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGGgcaagtgaag ... ctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG

EST: gi|148963920|gb|EE015037.2|EE015037

EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGG                         GGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGGgcaagtgaag ... ctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG

EST: gi|148930426|gb|EE284919.2|EE284919

EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGG                         GGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGGgcaagtgaag ... ctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG

EST: gi|149108940|gb|EE293053.2|EE293053

EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGG                         GGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGGgcaagtgaag ... ctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG

EST: gi|211327286|gb|FL017206.1|FL017206

EST:     GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGG                         GGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG
genomic: GGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGGgcaagtgaag ... ctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGG

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: 47 (upstream exon), 49 (downstream exon)
Score: 88

GAGTGCGCCTTCCCCATCTGCCGGGACTGCTACGAGTACGAGCGCCGCGAGGGCACGCAGAACTGCCCCCAGTGCAAGACCCGCTTCAAGCGCCTCAAGGgcaagtgaag ... ctgtttgcagGGTGCGCGCGCGTGCCCGGGGACGAGGAGGAGGACGGCGTCGACGACCTGGAGAACGAGTTCAACTGGAGCGACAAGCACGACTCCCAGTACCTCGCCGA

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 171

Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 99