ERISdb: a Database of Plant Splice Sites

General
Orthologs
EST
RNA-Seq

Sequence

atgc intronic sequence ATGC exonic sequence

GGCGCCCAACGCCGTCTACCGCGGCCGCCTCGACGGCGGGCGGCTCATCGCCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttgcgttgcttgcttcgtctggtttcctcccagcttggatctcgcaatgtgatgcagtgttgctgctgttgcag

Basic information

species	Zea mays
transcript	GRMZM2G054634_T01
intron #	2
splice site	5'
intron type	U2

Orthologous splice sites

atgc intronic sequence ATGC exonic sequence

upper sequence: GRMZM2G054634_T02 (Zea mays), 5'ss of exon 2
lower sequence: LOC_Os10g42110.1 (Oryza sativa), 5'ss of exon 2

GGCGCCCAACGCCGTCTACCGCGGCCGCCTCGACGGCGGGCGGCTCATCGCCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg-cgttgcttgcttcgtctggtttcctc---ccagcttggatctcgcaatgtga-tgcagtgttgctgctgttgcag----------
||| ||||||| ||||||||||||||||||||||||||| || ||||||||||||||||||||||| |||||||||||||| |||||||||||||||||||||    |   ||   ||  ||   || || |  | |    |  |        | || | | | |||  |  |  ||  ||||||           
GGCCCCCAACGTCGTCTACCGCGGCCGCCTCGACGGCGGCCGCCTCATCGCCGTCAAGCGCTTCTCCCGCCTCTCCTGGCCCGACCCGCAGCAGTTCCTCgtacctctcctcgcctctctctctctccggatctcgcaatgccacccatcctcctcactattactgcttttctcttgtggttgcattgcattgcag

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|71760095|gb|DR958032.1|DR958032

EST:     CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTC                         GCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC

EST: gi|211341381|gb|FL170566.1|FL170566

EST:     CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTC                         GCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCG
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCG

EST: gi|71426767|gb|DR807817.1|DR807817

EST:     CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTC                         GCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC

EST: gi|211341383|gb|FL170568.1|FL170568

EST:     CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTC                         GCGGAGGCG-CGGGCGTTGGGAAGGTGCGGGCACAAGCG
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGG-CACAAGCG

EST: gi|71330262|gb|DR801882.1|DR801882

EST:     CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTC                         GCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC

EST: gi|211343761|gb|FL170570.1|FL170570

EST:     CCGTYAAGCGCTTCTCGCGCCTCTCCTGGCCTGACC-GCAGCAGTTCCTC                         GCGGANGCGGCGGGCGTTGGGAAGGTGCG
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCG

EST: gi|78122641|gb|DV541025.1|DV541025

EST:     CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTC                         GCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC

EST: gi|71426768|gb|DR807818.1|DR807818

EST:     CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTC                         GCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC
genomic: CCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTC

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), 48 (downstream exon)
Score: 288

GGCGCCCAACGCCGTCTACCGCGGCCGCCTCGACGGCGGGCGGCTCATCGCCGTCAAGCGCTTCTCGCGCCTCTCCTGGCCTGACCCGCAGCAGTTCCTCgtatgatttg ... gctgttgcagGCGGAGGCGGCGGGCGTTGGGAAGGTGCGGCACAAGCGCCTCGTCAACCTCATTGGCTGCTGCGCCGAGGGTGACGAGAGGCTGCTTGTCGCCGAGTACA

Block sizes: 46 (upstream exon), 39 (downstream exon)
Score: 19

Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 20