ERISdb: a Database of Plant Splice Sites

General
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

AGGTCATTTAGCATACGCCCGTACATAATCCTGCTCTTCTCGCCAATCACAAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctccggcactccgctcgatctgttcctactagatgtgttgttcgtcttcaccgtcaatccacctcccccttactctgagtcgccttttgtttgcag

Basic information

species	Zea mays
transcript	GRMZM2G009894_T01
intron #	1
splice site	5'
intron type	U2

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|211369554|gb|FL313255.1|FL313255

EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCNAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

EST: gi|116829168|gb|EC865159.1|EC865159

EST:     TTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAA-CAGTC
genomic: TTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

EST: gi|211200178|gb|FL316755.1|FL316755

EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

EST: gi|211366908|gb|FL313254.1|FL313254

EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

EST: gi|116817813|gb|EC860723.1|EC860723

EST:     CGGACANTTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: CGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

EST: gi|211200179|gb|FL316756.1|FL316756

EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

EST: gi|211416484|gb|FL311420.1|FL311420

EST:     AAAAACCCTAAGCGCCGCCGGACAATTCGTTGCTCGCGATCCTCGCTTCG                         GGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC
genomic: AAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTC

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: 687

AGGTCATTTAGCATACGCCCGTACATAATCCTGCTCTTCTCGCCAATCACAAAAACCCTAAGCGCCACCGGACAATTCGTTGCTCGCGATCCTCGCTTCGgtaactctcc ... ttgtttgcagGGATCCGGAAGAGATGGCCAAGTCGAAGAACCACACGGCGCACAACCAGTCGTACAAGGCGCACAAGAACGGCATCAAGAAGCCCAAGCGCCACCGGCAG

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1165

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 873

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 607

Data associated with selected splice site

Sequence

Basic information

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments

RNA-Seq data