ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

CGTCGCCGTGCCCGCGGGAAGGTGGTCGGATGCGGCGCACCGGTTCTTGCGGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaaccgaccgaccgacgacctccgcactcttctgcttcttggaactgccaattcgttcctctgtttcctgagccatggtatctatctgtctgtgtcgcgtgcggctgttgatgattccag

Basic information

species	Zea mays
transcript	GRMZM5G865508_T02
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM5G865508_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os11g29710.1 (Oryza sativa), 5'ss of exon 2

CGTCGCCGTGCCCGCGGGAAGGTGGTCGGATGCGGCGCACCGGTTCTTGCGGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaaccgaccgaccgacgacctccgcactcttctgcttcttggaactgccaattcgttcctctgtttcctgagccatggtatctatctgtctgtgtcgcgtgcggctgttgatgattccag
|||||| ||||    |||   ||||||||| ||||| ||||||||||||||||||||||||||| |||||| |||||||||||||||| | |||||||||||  | |  |  || | |         | |  |  |||||||||| |  |||    || ||||     | || |  ||  || |  |     | | |||  |                       
CGTCGCGGTGCGGTGGGGCGCGTGGTCGGAGGCGGCTCACCGGTTCTTGCGGCGGTGCGCGGCCGCCGGCAGCCTCCACGCCTGCTACTTCCTCGGCATGgtgag-agtcacccaagc--------tccccttgctctgcttctttgctctgtttttttgttcg---atctcgtcggc--tgatggcggc--ggcggtgcag-----------------------

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|211325611|gb|FL040585.1|FL040585

EST:     GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATG                         GTGCTGTTCTACTGTATCGG
genomic: GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaacc ... atgattccagGTGCTGTTCTACTGTATCGG

EST: gi|211325613|gb|FL040587.1|FL040587

EST:     GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATG                         GTGCTGTTCTACTGTATCGGGGGCAGAGCGACGGGG-CGGCGCTACTGGCG
genomic: GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaacc ... atgattccagGTGCTGTTCTACTGTATCGGGGGCAGAGCGACGGGGGCGGCGCTACTGGCG

EST: gi|211325609|gb|FL040583.1|FL040583

EST:     GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATG                         GTGCTGTTCTACTGT
genomic: GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaacc ... atgattccagGTGCTGTTCTACTGT

EST: gi|211325602|gb|FL040576.1|FL040576

EST:     GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATG                         GTGCTGTTCTACTGTATCGGG
genomic: GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaacc ... atgattccagGTGCTGTTCTACTGTATCGGG

EST: gi|211325610|gb|FL040584.1|FL040584

EST:     GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATG                         GTGCTGTTCTACTGTATCGG
genomic: GGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaacc ... atgattccagGTGCTGTTCTACTGTATCGG

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 3 RNA-Seq libraries.

Block sizes: 28 (upstream exon), 22 (downstream exon)
Score: 1

CGTCGCCGTGCCCGCGGGAAGGTGGTCGGATGCGGCGCACCGGTTCTTGCGGCGGTGCGCGGCCTCCGGCAACCTCCACGCCTGCTACCTACTCGGCATGgtatgtaacc ... atgattccagGTGCTGTTCTACTGTATCGGGGGCAGAGCGACGGGGGCGGCGCTACTGGCGCGCTCGGCGGCGGGCGGGCACGCGGCGGCGCTGTACGCGCTCGCCGTGG

Block sizes: 43 (upstream exon), 47 (downstream exon)
Score: 26